Abstract: Separation grouting is an important means to reduce post-mining surface subsidence and prevent separation water disaster, in which the determination of grouting horizon is the primary problem of grouting engineering. It affects the effect of ground subsidence reduction and water disaster prevention. In the process of separation formation, different overburden structures have a very important impact on the development of separation. This paper takes the geological conditions of 11-3101 working face in Menkeqing Coal Mine as the engineering research background, based on the thin plate theory on Winkler’s elastic foundation, the calculation formula of vertical deflection of rock plate is derived. Meantime, the prediction model of the development horizon and spatial characteristics of overlying rock separation is established by combining with the theory of “key stratum”. At the same time, the three-dimensional discrete element technology is used to study the development law of the overlying rock separation of the working face. By carrying out the separation grouting project at the 11-3101 working face, drilling flushing fluid consumption observation and borehole color TV imaging technology are used to measure the development stratum of the separation. The reliability of the theoretical prediction and simulation model prediction results is verified by comparing the model prediction results and numerical simulation results with the measured results. At the same time, by observing the surface subsidence before and after grouting, the subsidence rate is reduced by 58.6%, and the grouting effect is significant. The model can provide more accurate layer selection for separation grouting and separation water disaster prevention.