[Objective] This study aims to address the issues of uneven spatiotemporal distribution of water resources and the difficulty in developing integrated urban-rural water supply in mountainous cities. Based on the connotation of integrated urban-rural water supply and the characteristics of its different development modes, this study innovatively constructs a coupling coordination evaluation indicator system and a zoning model for integrated urban-rural water supply. Taking the typical mountainous city of Chongqing as a case study, water supply zoning patterns with distinct regional characteristics are identified, and differentiated development schemes for urban-rural water supply are proposed. [Methods] Eight indicators were selected from three dimensions—current status of rural water supply engineering systems, natural geographical conditions, and socio-economic development. An “engineering-natural-economic” coupling coordination evaluation indicator system for integrated urban-rural water supply was constructed, and the Delphi method was used to determine the indicator weights. Considering the mutual constraints and synergistic effects among the three subsystems, a coupling zoning model for integrated urban-rural water supply was constructed. [Results] (1) The coupling coordination degree of each district and county ranged from 0.245 to 0.877. The coupling coordination degree intervals for the urban pipeline extension mode, regional pipeline interconnection mode, regional integrated block mode, and single-village upgraded point mode were [0.8, 1], [0.75, 0.80), [0.60, 0.75), and (0, 0.60), respectively. (2) All eight districts and counties under the urban pipeline extension mode were located in the main metropolitan area. These areas had relatively flat terrain and high population density, which was conducive to the construction of large-scale water supply projects and pipeline networks. Eight districts and counties under the regional pipeline interconnection mode were mostly located in the main metropolitan area, with a small number in the Three Gorges Reservoir area of northeastern Chongqing. These areas had abundant but unevenly distributed water resources. Interconnection of regional main water supply pipelines could achieve regional water resource complementarity and pipeline network connectivity. Five districts and counties under the regional integrated block mode were distributed in the main metropolitan area and the Three Gorges Reservoir area of northeastern Chongqing. In northeastern Chongqing, small reservoirs and ponds served as the main water sources, and the scale of water supply projects was small but had integration potential. Integrating surrounding small water supply projects could enhance regional water supply security. Thirteen districts and counties under the single-village upgraded point mode were mainly located in the Three Gorges Reservoir area of northeastern Chongqing and the Wuling Mountain area of southeastern Chongqing. Due to the large terrain relief in mountainous areas, water supply projects were significantly constrained by terrain. Rural areas were remote with dispersed population, making it difficult for large-scale water supply to cover them. This mode was suitable for point-based water supply targeting individual villages. [Conclusion] (1) Four development modes suitable for integrated urban-rural water supply in Chongqing City are proposed, namely the urban pipeline extension mode, regional pipeline interconnection mode, regional integrated block mode, and single-village upgraded point mode. (2) According to the zoning results, the urban pipeline extension mode relies on its high urbanization rate to achieve full water supply coverage. The regional pipeline interconnection mode addresses elevation difference issues through interconnected pipeline networks, the regional integrated block mode forms intensive water supply units by integrating small water sources, and the single-village upgraded point mode solves drinking water problems in areas with complex terrain through decentralized water supply. The research findings provide technical support for the construction of integrated urban-rural water supply in Chongqing City and are of significant importance for ensuring regional water supply security and promoting the high-quality development of the Chengdu-Chongqing Twin-City Economic Circle.