The traditional network clock protocol supported by the current train communication network can only achieve sub-microsecond time synchronization accuracy, which cannot meet the needs of the time synchronization accuracy of each node of the current train. Aiming at the above problems, this paper proposes to apply the precise clock protocol to the train communication network. In order to achieve high synchronization accuracy under the condition of low offset range, based on the traditional PI control algorithm, this paper proposes a multi-model PI control optimization algorithm in the improved clock servo system, and sets the threshold limit values of the proportional coefficient KP and the integral coefficient KI, The quantitative relationship between the threshold limit value and the PI output compensation value is derived to compensate for the offset of the slave node. Finally, taking a train communication network scene as the research object, modeling and simulation is carried out on the OMNeT++ simulation platform, and the offset value of the master and slave nodes is analyzed. Compared with the offset value obtained by the traditional PI control algorithm, the improvement value of the offset of each node in the train communication network is all within 30ns, and the offset can be as low as 1.38ns, which verifies the superiority of the proposed algorithm.