Deep mining practices are jeopardized by the recurrent instability and failure of roadways/multi-tunnels. This paper describes a case study of the mining-induced impacts on the stability and control strategy of overlying multi-tunnels with backfill mining in the Ping Dingshan No. 10 Coal Mine in Henan Province, China. To reveal the dynamic impacts of coal mining on the stability of overlying multi-tunnels, particularly in the process of mining cycle and after the overlying strata long-term stability period, a 3D finite element model was applied to explore the effect of longwall panel width, advancing distance, and backfill material’s compaction ratio (BMCR) on the multi-tunnels’ deformation characteristics. The results obtained demonstrate that failure and deformation of the overlying multi-tunnels become more pronounced with the increased longwall panel width and advancing distance, as well as with BMCR reduction. The ranking of deformation degree in the overlying multi-tunnels is as follows: main haulage roadway > auxiliary haulage roadway > main inclined shaft > rock crosscut > auxiliary inclined shaft. Using a 2D physical simulation experiment, a comprehensive analysis method and engineering design concept for the stability control of overlying multi-tunnels with backfill mining are put forward based on further research of the deformation characteristics of multi-tunnels using caving and backfilling method. The results obtained are instrumental to the stability control of overlying tunnels in deep mining practices with similar conditions.