Choosing the right structural model for projects in various fields has become an important subject of research, and adopting a suitable model has been recognized as crucial to a project's success. For public–private partnership (PPP) programs involving ecological compensation in the Chishui Watershed, implementers are required to give extensive considerations to balancing economic, societal, and ecological impacts and benefits, connected to numerous stakeholders. Any program model choice is made difficult by various influencing factors introduced by these stakeholders. This paper examines models of PPP eco-compensation programs in the Chishui Watershed, a region that faces an acute conflict between protection and growth, and is in urgent need of eco-compensation mechanisms. For this purpose, we have developed an indicator system with three hierarchical levels containing, respectively, two, five, and 18 indicator items. A list of feasible PPP models are chosen based on existing programs in the region. Analytic hierarchy process (AHP)/fuzzy analysis is used to establish an integrated decision-making framework. The suitability of the models in each field can then be ranked by their integrated decision score. The differences between models are also analyzed to find the main limiting indicators on PPP programs.