Motor-transmission coupled drive system is attractive for battery and hybrid electric vehicles. In such a system, the motor rotor is directly connected to the transmission input shaft and the active-synchronization technique is implemented to assist the speed synchronization; therefore, the gear-shifting characteristics are different from those of traditional manual and automated mechanical transmissions. In this work, we present a methodology for modeling the gear-shifting process and analyzing its characteristics in a motor-transmission coupled drive system. We treat the engaging of sleeve and desired clutch gear as a two-phase process—sleeve first interacting with synchro ring and then with clutch gear, respectively, and investigate all possible interaction ways in each phase. The movement of each part is governed by multibody dynamics, and the speed jumps caused by shifting impacts are described using the Poisson coefficient of restitution. We then develop a hybrid automaton (HA) model to couple the continuous-time evolutions and the discrete transitions of state variables, which cover all interaction ways of sleeve, synchro ring, and clutch gear. Based on this model, we carry out simulations in matlab to analyze the effects of two control parameters—the relative rotational speed of sleeve and desired clutch gear, and the shifting force—on shifting performance. Simulation and bench test results show that the optimal control parameters are located in the domain where the relative rotational speed is negative with small absolute value, which means the sleeve will not be locked out by synchro ring and can engage with the desired clutch gear smoothly.