As distributed systems such as automotive, medical, manufacturing automation become larger and more complex, it is difficult to test these systems. Also, the synchronization of distributed applications make the testing more difficult. In the Software-in-the-Loop (SiL) simulation, a synchronization method among clock of applications is provided for virtual hardware devices and environment. A typical synchronization technique is that a single global clock synchronizes local clocks of other sites but may make high accuracy but low performance in SiL simulation because synchronization occurs in all nodes when the global clock ticks. Also there are some issues of which node should be selected, how much time the global clock drifts when adding new sites, etc. In the paper, we propose a method of clock synchronization based on relative time to enhance the simulation performance.