Environmental flow requirement has been used to improve the downstream river ecosystem of the reservoir. Releasing environmental flow will cause economic losses. It is difficult to know the exact economic losses of improving the river ecosystem. For water resources managers, a more intuitive method to trade off the economy and ecosystem is necessary. Therefore, this study combined the Range of Variability Approach (RVA), Indicator of Hydrologic Alteration (IHA), and quantified economic losses to design a set of reservoir operation simulations that are close to the current situation. In the optimization model, storage was treated as a decision variable to compare the multi-objective results of different scenarios. Based on the flow data and economic data of Zengwen and Wushantou Reservoirs, the rules for water use were designed. There were three different scenarios in the optimization model that included different objective functions. The optimized objective functions included objectives such as human water shortage, economic benefit, and ecological objectives. In addition, this study focused on the defect of the RVA method. We proposed a simple method (IHA score indicator) to improve the RVA indicator. The IHA score indicator could support the RVA method and find out the reservoir operating storage rule curve that is more in line with the natural state. The reservoir operating storage rule curve of the optimized model results would provide the operating rules for the Zengwen and Wushantou Reservoir System. It would meet human and ecological needs to the greatest extent under unknown hydrological conditions in the future. According to the different scenarios, suitable reservoir operation rules could be arranged, which could provide water resources managers with a reference when making decisions.