The rate equations of fluorophore are solved with Runge-Kutta algorithm, and the process of the excitation and the depletion in stimulated emission depletion (STED) microscope is analyzed in detail. Gaussian shaped pulse is used to simulate ther excitation and the depletion process. The pump time versus the exciting time and intensity, the depletion time versus the intensity of depletion beam are calculated. With the simulation in an exciting and depletion period, the best synchronization delay time between the excited beam and the STED beam in STED microscope is achieved. These results will play an important role in the microscope setup.