The thermal glider’s changeable volume produces propelling force to power the glider’s descending and ascending through the thermocline. The different depth, thickness, and intensity of the thermocline at different seasons and locations affect the working processes of the glider’s power system. Based on the enthalpy method, a mathematical model of the underwater glider’s power system was established and the time efficiency of operation was introduced, so that the effects of different thermoclines on the underwater glider’s power system were analyzed theoretically. The simulation result shows that the thermocline affects the transition time of the phase change processes of working fluids within the thermal engine tubes. There exist the threshold values of the thermocline’s depth and upper thickness for the power system’s operation. A depth or upper thickness of the thermocline less than the corresponding threshold leads the power system to work abnormally. To keep the power system working efficiently, a glider must be kept in warm surface water for a certain period before it moves through cold water, so that the time efficiency of operation is reduced. A less time efficiency of operation is unfavorable to the thermal glider to penetrate through the ocean currents.