The overburden rock mining fissures are the main cause of coal spontaneous combustion, gas pooling, and mine water inrush caused by goaf air leakage. Rapid and accurate determination of the development and evolution law of mining fissures have great significance for the application of coal spontaneous combustion prevention and control, gas disaster prevention and control, and water damage prevention and control measures. In this paper, a preliminary judgment of the development height of the water-conducting fracture zone is made based on the theoretical analysis, and the physical model size of the numerical simulation is determined according to its judgment result. It is judged that the development height of its water-conducting fracture zone is between 49 and 64.2 m, which is in line with the actual results. Based on this, a three-dimensional solid model was established in PFC (Particle Flow Code) software to analyze the fissure development pattern of the overburden rock and the development height of the water-conducting fracture zone when the main key stratum of the rock seam is in different positions by simulating the excavation process of the coal seam. The results show that when the main key stratum is located in the “original crack belt boundary,” the development of water-conducting fracture zone is significantly inhibited; when the main key stratum is located in the “original caving zone,” the water-conducting fracture zone is fully developed, and the crack belt finally develops to the top of the model. In order to verify the accuracy of the numerical simulation, similar material simulation experiments were performed under the same scheme. The results are consistent with the numerical simulation conclusions, effectively verifying the accuracy of the numerical simulation. Finally, the extraction of porosity of the goaf was carried out based on numerical simulation, and the permeability zoning of the goaf was performed; the results show that the development of the water-conducting fracture zone has a significant influence on the permeability of the mining area, and the more fully developed the fissure is, the greater is its permeability. In this paper, the fissure development law in the goaf under different key stratums is explored by various research stratums, and the results show a good consistency, which provides a scientific basis for the prevention and control of disasters such as water inrush and coal and gas outburst in mines, and provides theoretical guidance for safe mining.