In e-commerce, as one of the most secure protocols, the SET protocol resolves some security issues. However, SET encryption and decryption program have gradually been doubted because of its lack of security guarantee. An improved elliptic curve cryptography is proposed to replace the original private key encryption algorithm which can improve the speed, performance, and security of the protocol. In this study, an improved NAF algorithm is proposed to develop the encryption and decryption speed of data affected by time-consuming ECC point multiplication. Compared with existing algorithms, the improved algorithm has better time complexity and it uses less computational resources. Besides, the MD5 hash generation algorithm is used to further improve the security of the existing elliptic curve cryptosystem.