Abstract: Overburden separation layer filling technology for ground surface subsidence control is an important part in the system of coal mine green mining. In this study, by considering the overburden structure and ground surface subsidence law, we propose a method for predicting the horizontal position of overburden separation layer over repeated mining inclined panel according to the maximum subsidence angle. The method of using the underground existing grouting pipeline system, drilling sites in main roadway, and inclined boreholes to fill overburden separation layer is proposed. Five drilling sites are arranged for the panel; in each drilling site, there are three inclined boreholes pointing to the separation layer under the sub-key layer, the soft and hard rock alternating zone between the sub-key layer and the main key layer, and the main key layer, respectively. The end hole is located near the maximum subsidence line. Field monitoring result shows that the maximum subsidence is 0.3 m after filling, indicating the filling technology proposed in this study is effective. Usually, it is difficult to identify the accurate locations of the key layers and the target areas of the separation layer due to the uncertainty of rock occurrence, the complexity of rock mass structure, and the testing accuracy of rock’s physical and mechanical properties. Therefore, when underground borehole-based grouting and filling technology is carried out, reasonable filling targets should be explored by the test processes of alternating drilling and grouting. The study is of significant to provide a reference for other underground borehole-based filling design under similar engineering geological conditions.