Abstract: Accurate identification of the grouting position in overburden isolated grouting and the reasonable determination of the protective layer thickness are of significant importance for preventing surface subsidence and protecting surface buildings and infrastructures. In order to realize the accurate grouting and reduce subsidence in multi-bed separation grouting. By improving the method for determining separation positions based on the composite beam theory, the filling positions for multi-bed separation grouting were determined. Using the theory of elastic thin plates, a structural mechanical model of the protective layer for overburden isolated grouting was established. An equivalent model for the grouting filling space of overburden isolated separation was constructed, and the minimum and maximum total volumes of the grouting filling space were determined according to the breaking law of the upper and lower rock layers in the grouting space. The effect of multi-bed separation grouting in “three soft” thick coal seams was evaluated through the use of probability integrals, combined with actual surface monitoring results. Additionally, 22151 working face of Peigou Coal Mine in Zhengzhou mining area was analyzed as case study. The results show that field borehole observation validated the accuracy of the bed separation positions. Multi-bed separation grouting was successfully implemented between the bottom of medium grained sandstone 152.6 m away from the coal seam and the bottom of fine-grained sandstone 168.6 m away from the coal seam. When the mining thickness of the working face is 7.1 m, a protective layer thickness of 25.2 m ensured the safe implementation of overburden isolated grouting. Theoretical grouting volume calculations range from approximately 9.5 × 10⁴ to 14.7 × 10⁴ tons while the actual engineering grouting volume for multi-bed separation grouting is approximately 13.3 × 10⁴ tons, with a grouting-to-mining ratio of about 0.41. The maximum surface subsidence is 649.8 mm, and the maximum horizontal deformation value of the surface at most residential buildings is within the Ⅰ degree of damage. The surface subsidence control effect of mining with multi-bed separation grouting was remarkable, and the subsidence reduction rate was about 77.91%.