The existence of water-bearing karst caves makes the movement law of coal seam overburden special. In order to study the influence of water-bearing karst cave on the movement of coal seam overburden, this paper takes a mine in Guizhou as the engineering background, uses FLAC3D to carry out numerical simulation research, and compares and analyzes the movement law of coal seam overburden under the action of karst cave with or without water content. The results show that: (1) In the case of water-bearing karst cave coal seam mining, the deformation and subsidence of the surrounding rock of the karst cave increased by 37.24% compared with the case without water. With the increase of the advancing distance, the karst cave near the bottom corner of the goaf appeared obvious sinking phenomenon, the right side of the karst cave appeared inward extrusion phenomenon, and the stress concentration area and failure area of the surrounding rock of the karst cave and the roof of the coal seam gradually penetrated. (2) Compared with the water-free condition, the overburden migration is strengthened under the water-bearing condition, in which the maximum curvature increases by 0.88 mm·m-2 and the maximum horizontal deformation increases by 1.81 mm·m-1. (3) With the advance of the coal mining face, the cracks in the surrounding rock of the water-bearing karst cave and the cracks in the coal seam roof continue to expand. When the horizontal distance between the working face and the karst cave is less than 10 m, the cracks in the surrounding rock of the karst cave and the cracks in the roof are connected to form water-conducting cracks. The research results have theoretical and engineering reference significance for roof management and surface subsidence prevention of coal seam mining under the influence of karst caves.