The importance of ecological benefit evaluation is widely recognized; however, the inconsistency of evaluation content and indicators has greatly affected the credibility of the evaluation results. Most of these results are reasonable but are difficult to be compared. Based on analysis of available relevant ecosystem evaluation methods, this paper proposes an ecological benefit evaluation framework that emphasizes that ecological, economic, and social benefits together constitute the value judgment standard and decision-making basis for human society. The ecological benefit is the foundation of economic and social benefit and should include the overall contribution of the ecosystem and consideration of ecosystem dynamics. The principles of selecting ecological benefit evaluation indicators include relevance, sensitivity, hierarchy, decision orientation, representativeness, feasibility, independence, economic applicability, and social acceptability. A multi-criteria synthesis method for selecting ecological benefit indicators and three criteria (quantifiable, specific, and surprising) for ecological benefit evaluation is proposed. As a preliminaries theoretical analysis, it can provide an important reference for the construction of ecological benefit indicator systems.