A coupled modes method is proposed to simulate the active mode locked laser. In this method, the electric fields of optical modes in the laser cavity are treated as free classical oscillators. The optical modulator provides the coupling among them. It is found that the eigenvalue of this coupled system is corresponding to the threshold optical gain, and the eigenfunction is corresponding to the optical field of each mode. The simulation results agree with the Master equation and experiments. Especially the model can be applied to the rational harmonic mode locking case by introducing the concept of ghost modes. The multitrip photons form a set of ghost modes or very weak oscillators. These ghost oscillators play the crucial rule working as the bridge to transfer energy and couple the real cavity modes/oscillators together. The model demonstrates both time domain pulse repetition rate multiplication and the frequency domain mode distribution. The proposed method will help understand the physics of rational harmonic mode locking mechanism and assist the design of devices such as optical pulse generator and multiwavelength laser. Therefore it should have great application in the optical signal generation and processing.