Engineering practice and real-life cases show that the geological conditions of the Guilin overlying karst site are complex. In particular, the groundwater, which drives the accelerated formation of soil cavities, and the thickness of the overlying soil layer, which affects the speed of the groundwater subsidence process. Therefore, this paper is based on a physical model to evaluate the effects of groundwater level changes caused by different factors on the deformation of karst cover. The model tests are simulated for different cover thicknesses (6 cm, 9 cm, 12 cm, 15 cm, 18 cm) under rainfall and other recharge, cavity supply, and drainage conditions at the same density (1.40 g/cm3) and initial water content (30%), respectively. The results show that with the increase of rainfall and other recharge time, the basic change trend of different cover thicknesses is that the infiltration curve changes faster at the beginning and slows down at the end, but the thicker the cover, the slower the overall deformation; at a certain rate of cavity recharge and drainage, the thicker the cover, the smaller the deformation caused by the fluctuation of groundwater level. The cavity recharge makes the cover displacement obvious, in the order of 0.304 cm, 0.173 cm, 0.118 cm, 0.068 cm, and 0.056 cm. After the formation of the cavity, the rainfall, other recharge, and the cavity supply and drainage accelerate the destruction and deformation of the soil body and the upward development of the cavity. The research results provide theoretical support for the subsequent prevention and control of karst collapse in covered karst areas, and have certain practical engineering significance.