Chinese megacity communities are not only the primary drivers of economic development but also epicenters of systemic contradictions compounded by overlapping risks. In recent years, NIMBY conflicts have arisen with growing frequency within urban communities, posing a severe threat to urban social sustainability and exposing the significant limitations of the traditional state-led governance model. While nonprofit organizations can compensate for governmental governance deficiencies, their mitigating mechanisms, functional boundaries, and contextual differences remain to be systematically examined. To address this gap, the present study conducts an empirical analysis using data from the Chinese Social Survey (CSS). Methodologically, the study applies OLS regression, mediation–moderation analyses, and heterogeneity tests. The findings reveal that: (1) Participation by nonprofit organizations is associated with significantly lower individual NIMBY opposition intent, thereby playing a mitigating role in alleviating NIMBY risks within Chinese megacity communities. (2) Trust in nonprofit organizations serves as a mediating pathway and acts as a social capital vehicle through which nonprofit organizations alleviate NIMBY risks by mitigating individual opposition. (3) Government information disclosure and institutionalized channels for residents’ participation significantly amplify the negative association between nonprofit participation and individual NIMBY opposition intent, thereby strengthening the mitigating efficacy of nonprofit organizations. (4) The mitigating effects exhibit marked community heterogeneity, indicating that the efficacy of nonprofit participation is highly contingent upon the specific governance resources and structural characteristics of the community. This study improves the theoretical framework of NIMBY risk governance and offers empirical evidence as well as practical guidelines for fostering sustainable urban governance in Chinese megacity communities.