In the rapid urbanization and land development process, the integration of urban and rural areas has accelerated. Alongside this trend, the sustainable operation of suburban villages in metropolitan areas face many difficulties and challenges, especially in terms of the efficient use of land and the coordination of stakeholders’ interests. However, there remains a lack of systematic case studies in the literature targeted toward suburban villages in metropolises. This study selects three typical suburban villages in the metropolis of Jiangning District, Nanjing (i.e., a metropolis in China) to narrow this research gap. We collected primary data based on field investigations, structural interviews, and professional documents. With three typical villages employed as comparative case studies, we developed a theoretical framework to systematically analyze the operation process and the challenges faced by suburban villages in the metropolis. The results revealed the different application scenarios of three stakeholder-led models, including the state-owned enterprise-led model, the grassroots government-led model, and the private capital-led model, in the sustainable operation of metropolis-based suburban villages. The findings shed new light on selecting an appropriate path to boost the sustainable endogenous development of rural areas. This study extends existing research on the sustainable operation of suburban villages in the metropolis, providing practical guidance on aligning stakeholder-led models to better integrate urban and rural areas.