The first phase of the South-to-North Water Diversion Project's Eastern Route (hereinafter referred to as the first phase project) is an important component of China's national water network, and the joint scheduling of the first phase project can address the spatiotemporal distribution discrepancy of water resources in China, thereby ensuring regional water security. This study aims to leverage the synergy of multiple engineering systems to overcome the bottleneck of insufficient regulation and storage capacities in single projects. It analyzes the basic background regarding the compensation scheduling of the first phase project, generalizes the engineering system, and establishes a compensation scheduling model. Subsequently, the study compares and analyzes the water shortages and electricity fees for water transfer in water-receiving areas under four scheduling modes: using only water from the Yangtze River, water compensation, storage compensation, and water‒storage combined compensation. It also reveals the laws of water compensation and storage compensation in different hydrologic years. The results indicate that the wetter the hydrologic year is, the more significant the effects of using water compensation; the drier the hydrologic year is, the more significant the effects of using storage compensation. Water compensation as well as water‒storage combined compensation have lower average electricity fees and smaller water shortages. Compared with water compensation, for every 1.0 × 10⁸ m³ of water shortage reduced in the high-, normal-, and low-flow years, combined compensation increases average electricity fees by 17.63 million CNY, 14.25 million CNY, and 9.01 million CNY, respectively. Therefore, it is more economical to adopt water compensation scheduling in wet years and water‒storage combined compensation scheduling in dry years. The research findings provide fundamental understanding for the joint scheduling of backbone projects in China's national water network, and offer engineering examples for optimizing its water resource allocation pattern.