During the water injection development process of highly deviated wells in low-permeability reservoirs, the water flooding distance between different layers of the same oil and water well is different due to the deviation of the well. In addition, the heterogeneity of low-permeability reservoirs is strong, and the water absorption capacity between layers is very different. This results in poor effectiveness of commonly used layered injection methods. Some highly deviated wells have premature water breakthroughs after layered water injection, which affects the development effect of the water flooding reservoirs. Therefore, based on the analysis and research of the existing layered injection allocation method and sand body connectivity evaluation method, considering the influence of sand body connectivity, the real displacement distance of highly deviated wells, reservoir physical properties, and other factors, a new methodology for determination of layered injection allocation in highly deviated wells drilled in low-permeability reservoirs is proposed. In this method, the vertical superposition and lateral contact relationship of a single sand body are determined using three methods: sand body configuration identification, seepage unit identification, and single sand body boundary identification. The connectivity coefficient, transition coefficient, and connectivity degree coefficient are introduced to quantitatively evaluate the connectivity of sand bodies and judge the connectivity relationship between single sand bodies. The correlation formula is obtained using the linear regression of the fracture length and ground fluid volume, and the real displacement distance of each layer in highly deviated wells is obtained. The calculation formula of the layered injection allocation is established by analyzing the important factors affecting the layered injection allocation, and a reasonable layered injection allocation is obtained. The calculation parameters of this method are fully considered, the required parameters are easy to obtain, and the practicability is strong. It can provide a method reference for the policy adjustment of layered water injection technology in similar water injection development reservoirs.