At present，the safety protection of intelligent substation system is mainly implemented according to IEC 62351 standard. As an international standard，its safety technology mainly adopts international algorithm RSA，AES and digital certificate. In view of the security defects of communication in intelligent substation system，this paper proposes the following three solutions： 1） the communication between intelligent substation equipment based on IEC 62351 security mechanism should adopt the national security algorithm and dispatching digital certificate technology； 2） finding out the security risks of communication protocol IEC104 from dispatching master station to substation，putting forward the security transformation scheme and implementation method； 3） putting forward the communication protocol transformation schemes of station control layer and the process layer，then implementing them by the national security algorithm and scheduling certificate technology. The above security measures can ensure the real-time，reliability，confidentiality，integrity and availability of communication information and information resources in the station，stop illegal access of unauthorized users，and ensure the authenticity of identities of both sides of communication and the traceability of business data.