This study used the "common pool resources" theory, "environment entitlement" theory, and "socio-ecological framework" to analyze how the existing institutions affect ecosystem management by communities and eventually the status of the ecosystem. To prove targeted policies, we eventually developed a context diagnostic tool for community resource use in protected areas. This tool is being updated and experimented in the Wuyishan National Park Pilot through knowledge co-production realized by communities' perception and researchers' observation. The key factors affecting resource accessibility mainly include land policy at the macro scale, protected area planning and management at the meso scale, and village convenance at the micro scale, indicating the combined effect of legal force and folk norms. The key institutions affecting access to ecosystem services and well-being include mainly the formal institutions, such as market and credit systems at the meso scale, and informal institutions that are long-formed for maintaining development, mainly through some collective actions. The study also suggests that a negotiation procedure is necessary to motivate communities' acceptance of new rules and participation in the construction of national park, during which the institutional changes are meant to sustain the ecosystem services. The negotiation thus aims to set management rules in a way that the (1) procedure is legitimate and fulfills the autonomy of the communities, (2) content respects the history and tradition, and is formed based on abundant available information, and (3) implementation of the agreement depends on clear cost-benefit analysis. In this way, the perception of ecosystem from communities may tend to converge with the goal of conservation. Therefore, the diagnostic tool can help prescribe targeted policies to improve ecosystem management during the experimental period in national parks, to reach a win-win goal for the integrity of ecosystem and human well-being through institutional change.