As a new application form of sustainable energy generation, building-integrated photovoltaics provide great flexibility for energy conservation and emission reduction. However, due to the randomness and volatility from photovoltaic generation, the full exploitation of the advantages of building-integrated photovoltaics has become an important question for the utilities. To address this issue, this paper proposes a novel and comprehensive (combined) water-energy supply system applied to the smart community with building-integrated photovoltaics and two-stage electric-hydraulic dispatching method. It was designed to minimize the electricity consumption cost and power fluctuation while meeting the water demand loads, followed by the iterative algorithm as well as linearized techniques to solve the optimisation model. The Shapley value method was introduced to ensure the fair revenue between the property company and owners. Simulation studies on a building-integrated-photovoltaics community and a 15-node water distribution system indicates that the annual operation cost of the water-electricity combined supply system was reduced by 29.6% while the external grid obtained a better prediction regarding the real-time exchange power. The results confirm the effectiveness of the proposed model on peak shaving and valley filling and fluctuation smoothing.