The invention discloses a time unification implementation method based on a Beidou satellite navigation system. A Beidou receiver and a time unification device which is connected with the Beidou receiver and provided with a data interface are provided, the time service function of the Beidou system is provided for a clock user, the structure is simple, and user-friendliness is achieved. To achieving the function, a clock source selection module, a clock learning correction module, a user-defined time generation module and a time distribution module are arranged, and a processing method for user-defined time generation and a processing method for clock source selection and clock distribution are achieved in combination with the Beidou system. The new clock source obtaining method which is simple, practicable and suitable for confidential use is provided for the clock user.