The Agricultural Environmental Conservation Program is a useful system for creating sustainable agriculture and environmentally friendly and comfortable rural areas. However, there are still many problems and difficulties, such as the establishment of necessary activities and plans by the residents themselves, and improvements are required. The degree of importance and difficulties according to the implementation stage of each stakeholder was quantified and compared with each other, and the specific difficulties recognized by on-site support organizations were structurally analyzed. It was analyzed that the importance and difficulties of the project implementation stage for local government officials and the project implementation planning stage for on-site support organizations were very high, indicating that they perceived the most need for improvement. On the other hand, 21 specific problems and difficulties were derived based on the results of the literature survey and stakeholder interviews. As a result of the structural analysis using the DEMATEL method, the most influential factor was the low understanding of the project by residents, the most influential factor was the lack of collecting and reflecting residents' opinions, the most central factor was the lack of collecting and reflecting residents' opinions, and the most causal factor was the lack of education and promotion of the project. The results indicate that a more stable system can be established if continuous promotion and education, periodic meetings and discussions, active reflection of residents' opinions in project implementation plans, and simplification of implementation inspection and project cost execution through the implementation inspection platform are promoted. Despite the limitations, considering that no institutional analysis of agricultural environmental conservation programs has been conducted so far, the results of this study are expected to serve as a basis for the establishment of relevant policies in the future.