Layer subdivision is currently one of the principal techniques employed to solve interlayer contradictions during water injection in multilayer heterogeneous reservoirs, but experimental research on the mechanism and the corresponding implementation plans is lacking. In this study, a multilayer heterogeneous core model was designed, and physical simulation experiments with different subdivisions and variation coefficients were conducted. Furthermore, the influence of the subdivision degree on the water injection development effect was analyzed, and the dynamic characteristics of the oil displacement of each sublayer were compared. Finally, the boundary standard of the layer subdivision was discussed. The results demonstrate that the water breakthrough appears rapidly in the high-permeability layer, and water channeling is easily formed after water flooding. The remaining oil is mostly retained in the low-permeability layer. Layer subdivision water injection can effectively reduce the high water cutoff and improve the oil recovery. The oil recovery increases with the layer subdivision degree, while the incremental rate decreases gradually. The low-permeability layer is observed to be the main layer contributing to the increase in the total recovery of multilayer reservoirs, with a contribution rate that initially increases and subsequently decreases with the increasing subdivision degree, from 0.9 to 11.9, and 29.8%, and subsequently drops to 15.1% during the general water injection with 2-, 4-, and 8-layer subdivision mining. The heterogeneity variation coefficient of 0.55 is used as the subdivision standard to divide different permeability layers to be developed as 1 layer in the multilayer heterogeneous reservoir.