The GIS-based water quantity and water quality model is widely used to provide decision-making supports for water resource and water quality management. However, the existing integration patterns of GIS and model system mainly depend on data communication between themselves which may lead to low operating efficiency and time-consuming model setup. In this paper, a generalized data structure (dual object structure (DOS)) which can store the data of GIS objects and model objects together is proposed and realized for the first time, avoiding frequent data communication during the period of numerical simulation and result expression, realizing the fusion of GIS objects and model objects at the data structure level, improving the operating efficiency of the system. Finally, the water quantity and water quality modeling software (digital basin simulation system (DBSS)) based on DOS was developed by using C++ language. The software has been applied successfully in large-scale river basins of China, and one of the cases was demonstrated to show the application process and the outstanding results.