This study aims to provide an integrated analysis of the diverse institutional logics and internal justification processes that underlie the sustainability of small schools in rural and agricultural communities in South Korea. Drawing on the theories of institutional logics and institutional work, a multiple case study was conducted at two small schools located in Jeollanam-do and Chungcheongbuk-do. The analysis revealed that multiple institutional logics coexist within these school organizations, resulting in differentiated roles among actors surrounding the schools. In response, actors actively negotiated school-community integration by engaging in identity work, ethical and emotional justification, and strategic blending of institutional logics. These practices contributed to the reconfiguration of both the organizational identity of the schools and their institutional status within the local community. The findings empirically demonstrate how rural small schools are evolving into complex, multi-functional organizations at the intersection of education, welfare, and regional revitalization. Theoretically, the study highlights how multilayered justification and relationship-based practices can serve as key drivers of institutional change. Based on these insights, the study calls for differentiated policy support strategies aligned with each school's institutionalization pathway, and recommends institutional enhancements such as place-based leadership and collaborative governance models to sustain relational and autonomous structures.