The invention discloses an FC network time synchronization method based on a complex network structure, and relates to the field of FC network time synchronization methods. The method comprises the steps that 1, device IDs and master clock ID values of all devices are set, the initial values are the device IDs, ID primitives are generated, and the priorities of all the devices are set; 2, the device sends an ID primitive and a time primitive to an adjacent device, and timing is started at the same time; step 3, the adjacent device receives and analyzes the ID primitive, and replies the ID _ RDY primitive to the device; 4, after receiving the ID _ RDY primitive sent by the adjacent device, the device stops timing and calculates the time difference; step 5, the devices are synchronized according to the set priorities and the master clock ID values of the synchronized devices are updated to complete priority transmission; according to the method, the problem that FC network time of a complex network structure cannot be synchronized due to the fact that priority of existing FC equipment cannot be transmitted is solved, and the effects of achieving priority transmission and time synchronization of all FC equipment are achieved.