In order to solve the problem of output power fluctuation of dynamic wireless charging system for electric vehicles based on short segmented guide rail structure, this paper analyzes the mechanism of power fluctuation, and proposes a power fluctuation suppression method and system synchronous control structure based on primary side equivalent mutual inductance parameter estimation and primary side control. In this paper, the topological structure, mutual inductance estimation method and control strategy are analyzed and calculated theoretically. The magnetic field parameters of the coupling mechanism are obtained by finite element analysis and the system simulation model is built. The simulation results show that the output voltage fluctuation range is less than 5%, which has a good performance.