Optimizing Rural Water Supply Network (RWSN) is the basis for improving rural people’s lives and improving people’s health. Currently, the RWSN in China is relatively backward and can no longer meet the needs of the unified management of rural water resources. To optimize the RWSN, this study innovatively established a Multi-Objective Optimization Mathematical Model (MOMM) of RWSN, combining economic factors and reliability. This experiment first analyzes the characteristics of the RWSN system and then establishes a MOMM of a water supply network. NSGA-II algorithm and LM algorithm are introduced to handle the multi-objective model. The research results show that compared to Web decision tools, the RWSN based on the LM-NSGA-II algorithm can save 5.4% of the total annual cost of water supply pipelines. Therefore, the MOMM of the rural water supply pipeline based on the LM-NSGA-II algorithm has better economy and reliability. The experiment aims to provide certain reference values for the optimal control of RWSN through this study.