A case study was conducted in the Datiangang Basin in Linhai City. The comprehensive benefits of water quantity and quality, and the key factors, including the basin’s terrain, the characteristics of sub-basins, the types of land use, and the population distribution were considered in the study. ArcGIS was used to analyze and calculate the key factors of rainstorm and water quality management in the basin, and the water system connectivity scheme was developed through runoff analysis in the Datiangang Basin of Linhai City. The MIKE11 model was used to build the runoff-hydrodynamic-water quality coupling model, and the optimal connectivity scheme based on the water quantity and quality control system was determined, in order to construct the rainstorm and flood safety and water quality safety pattern. The results show that the established one-dimensional coupled model has strong applicability in the Datiangang Basin, and the optimal scheme meets the requirements of flood drainage in the basin and enables the water quality compliance rate to exceed 90%.