The invention discloses a user identity authentication method, a system thereof and an identifying code generating maintenance subsystem; the invention also relates to a communication terminal which generates a user identifying code for the user who logs on an application system, uses a communication exchange machine to take the user identifying code as a calling number to call the user, and can display the information of the calling number; the application system acquires the calling number which is input by the user and displayed on the communication terminal, and the calling number is compared with the generated identifying code, so that user identity authentication is carried out. Therefore, the problems that identity authentication in the internet application system can not be normally implemented and widely applied caused by lost or delayed short massage, poor telephone voice receiving accuracy and higher cost which are easy to occur in the identity authentication way based on short massage and telephone voice are avoided, thus improving the reliability and working efficiency of user identity authentication.