This long-term study established a sustainable and resilient framework for enhancing organizational capacity and adaptability, based on adaptive thinking, for a school disaster prevention system (SDPS) for academic institutions located in a potential natural disaster area. Due to the movement of continental plates and the effects of tropical depressions, disasters occur frequently in Taiwan. We established a conceptual framework under aspects of organizational resilience for a SDPS for school institutions located in a potential disaster area under a choice experiment (CE) framework. We then evaluated the heterogeneity of staff perspectives on an adaptive disaster-mitigation program, as revealed by their preferences and estimated the marginal effects associated with various potential scenarios for such a program. We found that integrating stakeholder concerns about environmental issues, cooperating with local government drills, providing training to be disaster relief volunteers and cooperating with local government to implement disaster-prevention and protection projects were all valid program characteristics. This study also confirmed the existence of heterogeneity in the preferences of participants for adaptive management in SDPS context, as evidenced by their willing attitudes toward participation in education and training courses, participation in implementing disaster prevention and protection projects and undergoing training to be disaster relief volunteers. Specifically, the potential disaster prevention transformation program embodying these features was associated with the highest marginal willingness to work (MWTW). These outcomes can assist in the development and implementation of evaluation frameworks for organization-based management strategies in the context of SDPS.