This article is the result of treatments on ground fissures for environmental protection and scientific shallow coal seam mining. In the southwestern mining area of China, the traditional longwall mining method has caused a large area of surface sinkhole, ground fissures, vegetation deterioration and disorderly coal gangue. To solve these problems, an integrated treatment technology that includes ground fissure treatment technology and underground backfilled technology was proposed as a solution. The technical principle and technical process were explained in detail; the ground fissure treatment technology involves a “three-step treatment method”, and the underground backfilled technology adopted a strip mining method with backfilling technology. The compression mechanical behavior of backfilled material, including coal gangue, fly ash and ordinary Portland cement, was studied; the mixed ratio of 1:0.3:0.18 was selected. In addition, the vertical stress, vertical displacement and plastic zone of the coal pillar were determined by FLAC3D numerical simulation, and a rational mining scheme of “11 m mining width, 2 m coal pillar width” was determined to be appropriate because of the lower vertical stress, smaller vertical displacement and better supporting capacity of the coal pillar. The monitoring results of ground sinkhole indicated that the maximal ground sinkhole deformation was 17.3 cm, and the deformation showed few changes after this technology was implemented. The treatment capacity of coal gangue and fly ash reached 821.150 t per year, and the vegetation survival rate of the ground fissure treatment area reached 85%. This integrated treatment technology could effectively control ground fissures and surface sinkhole as well as protect the environment.