In this paper, we propose a method to improve accuracy of equivalent system of a nonlinear system with time delay by an estimate which is based on the synchronization error. It is known that it is difficult to investigate this system by analytical methods, because this system is described by a difference-differential equation which is usually difficult to solve. We regard this system as an original system, and an assumed system without time delay as an equivalent system. To analyze the original system, we have already introduced an averaging method for the functional differential equation. Applying this averaging method, we construct the equivalent system. And an coefficient of this system is determined that behavior of the averaged system of the equivalent system coincide with that of the original system. We compare the equivalent system with the original system by the estimate which is based on the synchronization error. In order to improve the accuracy, we modify system parameters of the equivalent system so that the synchronization error is minimized. The result shows that behavior of the modified equivalent system remarkably is in good agreement with behavior of the original system.