In the filling process, layered phenomena often occur in cemented waste rock backfill, which may affect the filling effect. Therefore, it is of great significance to study the filling effect of layered backfill. In this study, the cemented waste rock backfill was sliced to analyze the aggregate distribution characteristics of different layers in the backfill. Subsequently, through numerical simulation, the influence of layered and non-layered cemented waste rock backfill on the filling effect of goaf was compared and analyzed. The study found that: (1) Non-layered backfill performs better in terms of roof support, roof subsidence, side wall stress, and internal stability, providing a more stable support effect, reducing roof subsidence, lowering side wall stress, and ensuring the safety of mining operations. (2) The stress in the middle of the roof of non-layered backfill is slightly higher than that of layered backfill, but the stress distribution on both sides of the roof is more uniform, providing a more stable roof support; the degree of roof subsidence is significantly smaller, and the support effect is better than that of layered backfill; the side wall stress is uniform with small displacement, whereas the side wall stress of layered backfill is greater with uneven displacement. (3) The presence of more fine aggregates in the upper layer of layered backfill makes it more susceptible to pressure deformation, while the uniform distribution of waste rocks in non-layered backfill provides a stronger overall load-bearing capacity with relatively small deformation. In conclusion, non-layered cemented waste rock backfill demonstrates superior support and stability in goaf, therefore, efforts should be made to control the layered phenomena in backfill composition, providing crucial support for mining operations.