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According to security demands of video conference system, this paper presented three schemes to encrypt parts of video data using permutation code and DES encryption algorithm based on the newest coding standard H.264. Comparing with encryption effects of three encryption schemes using two encryption algorithms respectively, this paper determined one of three schemes as a last encryption scheme. This encryption scheme adopts permutation code encryption algorithm to encrypt parts of motion vector residuals after transform and quantization before entropy encoding, and some codewords of DCT coefficients of residual data in the code stream, which includes TrailingOnes signs Levels and RunBefore. It has high security good real-time lower data expansion rate and good form compatibleness by theory analysis and experiment results, so it can guarantee video data safety and real-time to transmit and has a wide application value . In order to improve the encryption effect, the paper submits to apply this encryption scheme to the hardware in future.