The invention discloses a dual-board system time synchronization method, comprising the steps of: clock synchronous source selection: based on an indication sent by an in-band clock synchronous reference source of each path of IEEE 1588V2, and aided by hardware performance statistic data, finally selecting an optimal path of clock synchronous reference source as a clock synchronous source; clock synchronous source time delay compensation: performing time delay compensation on an IEEE 1588V2 link; system time synchronous message generation: obtaining a time synchronous source message and generating a time synchronous message; and system inner time synchronization: distributing the time synchronous message to each unit to perform system inner time synchronization. The dual-board system time synchronization method synchronizes the time of two mainboards or two systems of one device of an intelligent substation, and solves time synchronization of a present dual-board system device.