A user identification method and a system thereof are provided. A user device delivers a certificate packet with a user identification number to a certificate server, and receives a reply packet with a code from a password server. The user device uses the code to produce a user terminal identification code, and delivers an identification packet with the user terminal identification code to the certificate server. After having received the certificate packet, the certificate server delivers an inquiry packet with the user identification number to the password server, for the password server to inquire about the password and expiration time according to the user identification number. After having received the identification packet, the certificate server verifies the validity of the user terminal identification code and the expiration time with a database to determine whether the user is allowed to proceed to the subsequent transaction.