SET protocol plays a vital role in the payment field of Internet and mobile Internet. This protocol, by properly treating the relationship among between the users,merchants,payment gateway,acquirers, issuers,provides a safe and reliable protection for the process of the entire network payment. However,there are still some problems in efficiency and application of the SET protocol for its design limitation in its times. The security of the SET protocol in mobile payment is studied,and on the basis of ensuring the safety of original SET protocol,an improved scheme is proposed. The most important feature of the scheme lies in that OTP(One-Time Password) technology in the SET protocol process, the implementation status of the SET protocol is improved. Experiment and analysis indicate that the improved scheme is safe and efficient,and could fairly ensure the security of online payment.