Owing to the shortcomings of blindness and inaccuracy when backfilling in goafs and based on the key stratum theory, we propose the “multi-arch pier-column” backfilling method. This method involves drilling holes at specific locations on the surface to inject filling and slurry materials into the goaf and separation area under the key stratum. This allows the broken gangue to be cemented to form a stone body, to improve its overall strength. This process, along with filling in the separation area under the key stratum, ensures that the key stratum does not break, forming a joint medium of “separation area filling body + backfilled pier-columns + key stratum + coal column”, which prevents new subsidence on the surface layer. Using the Gaojialiang coal mine as an example, the effects of the proposed method on controlling surface subsidence were determined using a numerical simulation based on FLAC3D simulation software. The results indicate that this method can effectively control the key stratum and ensure that the surface subsidence is within a safe range. The multi-arch pier-column backfilling method utilises the self-bearing capacity of the overburden structure and greatly reduces the backfilling workload and the cost of backfilling for controlling surface subsidence. At present, the multi-arch pier-column system of the new backfill method is an unexplored and new area of research.