In order to study the optimal scheme of staggered distance mining in double coal seam and its influence on the key strata of overburden structure, take the geological conditions of Yushen Mine Area as the background, the optimal scheme was selected from the five simulation schemes of staggered distance mining by the FLAC3D numerical simulation method. Based on the Mohr-Coulomb strength criterion and numerical simulation results, the influence of different staggered distance on the key strata of overburden structure was discussed. The results show that the tensile stress of overburden strata on the working face shows a “valley-peak-valley” distribution with double coal seam staggered distance mining, the maximum principal stress in the influence range of staggered distance coal pillar shows a “flat peak” distribution, and the subsidence value shows a “peak” distribution. The optimal staggered distance is 40 m and the most unfavorable staggered distance is 0 m. Through the optimization of the staggered distance scheme of double coal seam mining, the integrity of the key strata of overburden structure can be effectively protected and the failure range of overburden structure can be reduced.