To reasonably allocate emergency supply reserve warehouses and enhance the utilization efficiency of emergency supply reserves, this paper proposes a new optimization method for the site selection of emergency supply reserve warehouses based on gray system theory—the multi-attribute weighted intelligent gray target decision-making evaluation model. This method innovatively incorporates the density of road networks, population density, economic density, and post-disaster response capability as key indicators. It then utilizes the multi-attribute weighted intelligent gray target decision-making evaluation model to evaluate the synthetic effect. Based on the evaluation results, optimization recommendations for the site selection of emergency supply reserve warehouses are provided. To validate the credibility of the proposed method, a comparative analysis is then conducted using the EEM-TOPSIS and TOPSIS–Gray Correlation Degree methods, resulting in largely consistent evaluation results. The study demonstrates that the multi-attribute weighted intelligent gray target decision-making evaluation model accounts for both hitting-the-target and missing-the-target scenarios for effect values and vectors of objectives. This approach effectively addresses the limitation of traditional multi-attribute evaluation methods, which can only rank evaluation schemes without effectively distinguishing between superior and inferior ones. This method also proves to be more user-friendly compared to others.