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In terms of both economy and sustainability, rural areas can greatly benefit from adopting E-commerce. The Chinese government is currently devoting significant efforts to developing agricultural E-commerce. However, one of the most significant problems is the lack of effective tools for evaluating regional potentials in this regard, possibly leading to inappropriate policymaking, investment allocation, and regional planning. To address this issue, this study proposes a novel and effective method for evaluating regional potentials for agricultural E-commerce development, integrating the method based on the removal effects of criteria (MEREC), Heronian mean operator, and combined compromise solution (CoCoSo) method. The method’s effectiveness is then tested and confirmed in the Chinese city of Yibin through an evaluation of its ten regions. The results suggest that such a method is robust, objective, and able to consider indicator interactions effectively. By applying this method, regional agricultural E-commerce development potentials can be thoroughly evaluated and ranked. This study contributes to the literature by providing new analytical techniques for agricultural studies, as well as by supporting political and investment decision-making for governments and E-commerce practitioners in the agriculture sector.