As a key node in the promotion of the “Western Development” strategy in Xinjiang, China, the large-scale mining of coal resources is bound to cause a series of ecological and environmental problems, such as surface subsidence. Desert areas are widely distributed in Xinjiang, and from the perspective of reserves and sustainable development, it is crucial to fully utilize desert sand to make filling materials and predict its mechanical strength. In order to promote the application of High Water Backfill Material (HWBM) in mining engineering, a modified HWBM doped with Xinjiang Kumutage desert sand was used to prepare a desert sand-based backfill material, and its mechanical properties were tested. The discrete element particle flow software PFC3D is used to construct a three-dimensional numerical model of desert sand-based backfill material. The parameters such as sample sand content, porosity, desert sand particle size distribution, and model size are changed to study their impact on the bearing performance and scale effect of desert sand-based backfill materials. The results indicate that a higher content of desert sand can effectively improve the mechanical properties of HWBM specimens. The stress–strain relationship inverted by the numerical model is highly consistent with the measured results of desert sand-based backfill materials. Improving the particle size distribution of desert sand and reducing the porosity of filling materials within a certain range can significantly improve the bearing capacity of desert sand-based backfill materials. The influence of changing the range of microscopic parameters on the compressive strength of desert sand-based backfill materials was analyzed. This study provides a desert sand-based backfill material that meets the requirements of mine filling, and predicts its strength through numerical simulation.