主要差异如下：
1、 对于待加密解密的数据，各自的填充模式不一样
C#的模式有：ANSIX923、ISO10126、None、PKCS7、Zero，而Java有：NoPadding、PKCS5Padding、SSL3Padding
2、 各自默认的3DES实现，模式和填充方式不一样
C#的默认模式为CBC,默认填充方式为PKCS7; java的默认模式为ECB，默认填充方式为PKCS5Padding
3、 各自的key的size不一样
C#中key的size为16和24均可；java中要求key的size必须为24；对于CBC模式下的向量iv的size两者均要求必须为8
翻看了3DES的原理：
DES主要采用替换和移位的方法,用56位密钥对64位二进制数据块进行加密,每次加密可对64位的输入数据进行16轮编码,
经一系列替换和移位后,输入的64位转换成安全不同的64的输出数据
.
3DES:是在DES的基础上采用三重DES,即用两个56位的密钥K1,K2,发送方用K1加密,K2解密,再使用K1加密.接收方使用K1解密,K2加密,再使用K1解密,
其效果相当于密钥长度加倍.
于是尝试在java中，对key进行补位，即用前8个字节作为byte[24] 中的byte[16]~byte[23];发现与c#中加密的结果相同！于是大胆假设C#中可能是检查key的size为16的时候
自动将前8个字节作为k3进行了补位，而java没有实现这一点（因为java的3DES算法中强制要求key的size必须为24）。这样的情况下，可能就是发送方用k1加密、k2解密、k3再加密；接受方k3解密、k2加密、再k1解密来实现。
最终经过编码验证，确认key大小为24时，java和c#的加密解密结果相一致。
Java中实现时，只要注意对大小不足24的key进行补位，和采用CBC模式，填充模式为PKCS5Padding即可。
public static byte[] encrypt(String sKey, byte[] bIV, byte[] bPlainText, int nOffset, int nSize)
throws Exception {
byte[] bKey = buildKey(sKey);
byte[] bInput = buildInput(nSize, bPlainText, nOffset);
byte[] bResult = encrypt(bIV, bKey, bInput);
return bResult;
}
public static byte[] decrypt(String sKey, byte[] bIV, byte[] bCipherText)
throws Exception {
byte[] bKey = buildKey(sKey);
SecretKey securekey = buildSecretKey(bKey);
IvParameterSpec iv = new IvParameterSpec(bIV);
Cipher cipher = Cipher.getInstance("DESede/CBC/PKCS5Padding");
SecureRandom sr = new SecureRandom();
cipher.init(Cipher.DECRYPT_MODE, securekey, iv, sr);
byte[] bOutput = cipher.doFinal(bCipherText);
int nLen = 0;
nLen = nLen | (int) bOutput[0];
nLen = nLen | ((int) bOutput[1] << 8);
if (nLen > bOutput.length - 4) {
throw new Exception("非法的密文");
}
byte[] bResult = new byte[bOutput.length - 4];
bResult = Arrays.copyOfRange(bOutput, 2, bOutput.length - 2);
return bResult;
}
private static byte[] md5Digest(String sData) throws NoSuchAlgorithmException {
MessageDigest md5 = MessageDigest.getInstance("MD5");
byte[] bData = sData.getBytes();
md5.update(bData, 0, bData.length);
byte[] hash = md5.digest();
return hash;
}
private static byte[] buildInput(int nSize, byte[] bPlainText, int nOffset) {
byte[] bInput = new byte[nSize + 4];
for (int i = 0; i < bPlainText.length; i++) {
Arrays.fill(bInput, 2 + i, 2 + i + 1, bPlainText[i]);
}
int usCRC = CCRC16.CalcCrcCheckSum(bPlainText, nOffset, nSize);
bInput[0] = (byte) (nSize & 0xFF);
bInput[1] = (byte) (nSize >> 8 & 0xFF);
bInput[nSize + 2] = (byte) (usCRC & 0xFF);
bInput[nSize + 3] = (byte) (usCRC >> 8 & 0xFF);
return bInput;
}
private static byte[] buildKey(String sKey) throws NoSuchAlgorithmException {
byte[] bTmp = md5Digest(sKey);
byte[] bKey = new byte[24];
System.arraycopy(bTmp,0,bKey,0,bTmp.length);
System.arraycopy(bTmp,0,bKey,16,8);
return bKey;
}
private static SecretKey buildSecretKey(byte[] bkey) throws InvalidKeyException,
InvalidKeySpecException, NoSuchAlgorithmException {
DESedeKeySpec dks = new DESedeKeySpec(bkey);
SecretKeyFactory keyFactory = SecretKeyFactory.getInstance("DESede");
SecretKey securekey = keyFactory.generateSecret(dks);
return securekey;
}
private static byte[] encrypt(byte[] biv, byte[] bkey, byte[] input) throws Exception {
SecretKey securekey = buildSecretKey(bkey);
IvParameterSpec iv = new IvParameterSpec(biv);
Cipher cipher = Cipher.getInstance("DESede/CBC/PKCS5Padding");
SecureRandom sr = new SecureRandom();
cipher.init(Cipher.ENCRYPT_MODE, securekey, iv, sr);
return cipher.doFinal(input);
}
}
class CCRC16 {
public static int CalcCrcCheckSum(byte[] pBuffer, int nOffset, int nSize) {
int[] table = {
0x0000, 0xC0C1, 0xC181, 0x0140, 0xC301, 0x03C0, 0x0280, 0xC241,
0xC601, 0x06C0, 0x0780, 0xC741, 0x0500, 0xC5C1, 0xC481, 0x0440,
0xCC01, 0x0CC0, 0x0D80, 0xCD41, 0x0F00, 0xCFC1, 0xCE81, 0x0E40,
0x0A00, 0xCAC1, 0xCB81, 0x0B40, 0xC901, 0x09C0, 0x0880, 0xC841,
0xD801, 0x18C0, 0x1980, 0xD941, 0x1B00, 0xDBC1, 0xDA81, 0x1A40,
0x1E00, 0xDEC1, 0xDF81, 0x1F40, 0xDD01, 0x1DC0, 0x1C80, 0xDC41,
0x1400, 0xD4C1, 0xD581, 0x1540, 0xD701, 0x17C0, 0x1680, 0xD641,
0xD201, 0x12C0, 0x1380, 0xD341, 0x1100, 0xD1C1, 0xD081, 0x1040,
0xF001, 0x30C0, 0x3180, 0xF141, 0x3300, 0xF3C1, 0xF281, 0x3240,
0x3600, 0xF6C1, 0xF781, 0x3740, 0xF501, 0x35C0, 0x3480, 0xF441,
0x3C00, 0xFCC1, 0xFD81, 0x3D40, 0xFF01, 0x3FC0, 0x3E80, 0xFE41,
0xFA01, 0x3AC0, 0x3B80, 0xFB41, 0x3900, 0xF9C1, 0xF881, 0x3840,
0x2800, 0xE8C1, 0xE981, 0x2940, 0xEB01, 0x2BC0, 0x2A80, 0xEA41,
0xEE01, 0x2EC0, 0x2F80, 0xEF41, 0x2D00, 0xEDC1, 0xEC81, 0x2C40,
0xE401, 0x24C0, 0x2580, 0xE541, 0x2700, 0xE7C1, 0xE681, 0x2640,
0x2200, 0xE2C1, 0xE381, 0x2340, 0xE101, 0x21C0, 0x2080, 0xE041,
0xA001, 0x60C0, 0x6180, 0xA141, 0x6300, 0xA3C1, 0xA281, 0x6240,
0x6600, 0xA6C1, 0xA781, 0x6740, 0xA501, 0x65C0, 0x6480, 0xA441,
0x6C00, 0xACC1, 0xAD81, 0x6D40, 0xAF01, 0x6FC0, 0x6E80, 0xAE41,
0xAA01, 0x6AC0, 0x6B80, 0xAB41, 0x6900, 0xA9C1, 0xA881, 0x6840,
0x7800, 0xB8C1, 0xB981, 0x7940, 0xBB01, 0x7BC0, 0x7A80, 0xBA41,
0xBE01, 0x7EC0, 0x7F80, 0xBF41, 0x7D00, 0xBDC1, 0xBC81, 0x7C40,
0xB401, 0x74C0, 0x7580, 0xB541, 0x7700, 0xB7C1, 0xB681, 0x7640,
0x7200, 0xB2C1, 0xB381, 0x7340, 0xB101, 0x71C0, 0x7080, 0xB041,
0x5000, 0x90C1, 0x9181, 0x5140, 0x9301, 0x53C0, 0x5280, 0x9241,
0x9601, 0x56C0, 0x5780, 0x9741, 0x5500, 0x95C1, 0x9481, 0x5440,
0x9C01, 0x5CC0, 0x5D80, 0x9D41, 0x5F00, 0x9FC1, 0x9E81, 0x5E40,
0x5A00, 0x9AC1, 0x9B81, 0x5B40, 0x9901, 0x59C0, 0x5880, 0x9841,
0x8801, 0x48C0, 0x4980, 0x8941, 0x4B00, 0x8BC1, 0x8A81, 0x4A40,
0x4E00, 0x8EC1, 0x8F81, 0x4F40, 0x8D01, 0x4DC0, 0x4C80, 0x8C41,
0x4400, 0x84C1, 0x8581, 0x4540, 0x8701, 0x47C0, 0x4680, 0x8641,
0x8201, 0x42C0, 0x4380, 0x8341, 0x4100, 0x81C1, 0x8081, 0x4040,};
byte[] bytes = pBuffer;
int crc = 0x0000;
for (byte b : bytes) {
crc = (crc >>> 8) ^ table[(crc ^ b) & 0xff];
}
return crc;
}
还有一种让Java和.Net兼容的方式,在.Net中指定模式为ECB，填充为PKCS7,然后在Java中采用其默认的模式（DESede/ECB/PKCS5Padding）即可,注意双方约定key的size为24个字节。建议双方对key以base64编码字符串进行告知，因为java和.net中byte字节的范围不相同(前者-128~127,后者0~255)，避免不必要的处理。
参考引用：http://gaoge2000.blog.hexun.com/18731819_d.html