Abstract: Presently, most water engineering scheduling systems are customized for specific watersheds, and are difficult to apply to other watersheds with different characteristics.This article mainly introduced a topological design method for water engineering scheduling systems using graph databases to achieve consistent descriptions for various types of watersheds.In this research, the topological structure of water objects was defined using the "node-attribute-link" in CQL language.Compared with traditional tree-based data structure storage, graph databases can significantly improve the analysis procedures for dealing with large and complex datasets.Based on this topology design approach, a topology-driven engine was proposed and verified through core technical processes, including data processing, program task scheduling, and parallel computing.Furthermore, a set of water resources decision-making platforms had been developed to adapt to various types of watershed topology, offering a new model for the construction of water engineering scheduling systems.The successful application of this method in various river basin systems has demonstrated that it significantly improves the adaptability of water engineering dispatching systems across different river basin scenarios and efficiently supports the construction of digital twin watersheds.