In the time synchronization of cluster collaborative navigation system, due to the dependence on the monad information transmission link of network master node, the node time synchronization accuracy is reduced when the fluctuation and the state of the master node is suddenly abnormal, which seriously affects the cooperative unity performance of the cooperative navigation system. The time difference estimation method for multi-node fusion in the cluster collaborative is proposed to solve the problem of time difference estimation fluctuations or inability to synchronize in the process of network time transfer relying only on the time center, and gives the verification conclusion of the actual experiment. The feasibility of the method is verified by the implementation of the method in the cluster collaborative navigation system and the field test.