The International Space Station (ISS) provides a reliable platform for the Alpha Magnetic Spectrometer (AMS) operating in orbit. However, the thermal environment of AMS can be affected by the ISS maneuvers during its operation. Locking solar arrays occurs most frequently and has considerable thermal effect on AMS by blocking the solar illumination on them. In this paper, the thermal network method was applied to numerically investigate the effect of locking solar arrays on the external heat fluxes and corresponding temperature response characteristics of AMS main radiators in ISS normal flight attitude +XVV by a system-level thermal model. The temperature increment model is established under solar arrays locked theoretically. The numerical results reveal that, the variation of ISS orbital altitude can cause the maximum decreasing of the external heat flux by 17.0% when locking solar arrays vertically, and the locking modes of solar arrays lead to the maximum reduction of external heat flux by 56.6%. In addition, locking solar arrays can cause the maximum drop of 9.0 °C on the AMS main radiators.