This paper focuses on the synchronization of multi-agent systems with Van der Pol oscillators as agents. As the Van der Pol oscillator has a limit cycle, by analyzing the system state near the limit cycle, the synchronization problem is transformed into the local stability problem of the error dynamical system. In particular, the convergence conditions of the error dynamical system can be obtained by investigating the properties of state transition matrix of a single period of the limit cycle. Furthermore, the simulation is conducted to verify the analysis.