We develop a moving-mesh permafrost model that contains a ground subsidence computation module to estimate the effects of ground subsidence on permafrost simulation under different warming scenarios. Including the ground subsidence process in the permafrost simulation produces only a relatively small improvement in the simulation performance of the ground temperature field, as validated by observations from two sites on the Qinghai–Tibetan Plateau (QTP). It is shown that ignoring ground subsidence tends to achieve a larger active layer thickness (ALT) but a smaller original thickness of permafrost that has thawed when simulating permafrost changes in a warming climate. The heat consumed by permafrost changes will be underestimated in simulations that do not consider ground subsidence. The effects that ground subsidence exerts within the permafrost simulation are clearly demonstrated under a strong warming scenario, which will influence the global energy budget. Projections indicate that the permafrost in the continuous permafrost area of the QTP may be close to the phase transition temperature to become zero thermal gradients in 2030–2040 under the SSP5-8.5 scenario, and there will be a great risk of ground subsidence by that stage. For permafrost regions with rich ground ice, the downward propagating temperature signals caused by ground subsidence are more attenuated. However, the heat calculation error will be larger in a simulation that does not consider ground subsidence there. This study quantifies the effects of ground subsidence, which can provide a better understanding of the permafrost thaw and energy budget of the QTP.