An ecotourism system that is based on wildlife habitats in ecological systems is considered a social-ecological system that has a feedback relationship with social systems. Increases in socioeconomic activities and tourism infrastructure construction are not conducive to the resilience of wildlife habitats, thereby stressing the ecological system and threatening sustainable ecotourism. Managing resilient wildlife habitats by developing transformation plans that can be used to construct new systems through self-organization and the absorption of stress is paramount to perpetuating sustainable ecotourism systems. This study aims to establish transformation plans to enhance the resilience of systems thinking regarding wildlife habitats. Such thinking involves the sequential application of dynamic thinking, causal thinking, closed-loop thinking, and the discovery of strategies. This study examines the case study of Eulsukdo Island in South Korea, and the following transformation plans are derived: (1) high-quality eco-education programs to help tourists become hard ecotourists; (2) subsidies for foraging area restoration; (3) ecosystem services of wildlife habitats; and (4) governance organization led by multiple actors. The results of this study can provide guidelines for the effective use of natural resources at ecotourism destinations and for the ecotourism development of damaged wildlife habitats.