The utility model discloses a security certification system based on a directory. The system comprises a directory server. The directory server is connected with an identity management server through a synchronous interface module. The identity management server is connected with a mobile terminal. The mobile terminal sends an intelligent card to a user. The intelligent card is connected with a client. The client is connected with an identity certification device through a communication interface module. The identity certification device is successively connected with a data storer and a host computer. The identity management server is connected with the client. The system achieves an identity certification function of a user in a portal system, ensures security and confidentiality of information transmission in a user certification process, ensures the information to be authentic, reliable and free of repudiation, and achieves combination of identity certification and information security storage.