In this paper, the nature-based tourism is described as one of the tools to achieve sustainable development in small islands. The study was carried out at Ayer, Bidadari and Onrust Islands of Kepulauan Seribu chains at Jakarta Bay, Indonesia. While the historical records show that previous uses of such islands have started at sixteen century, tourism uses was started at the beginning of 1970s. Among nature-based tourism destination in Kepulauan Seribu chains, these islands are the famous destinations and received a lot of tourists. Tourism growth at these islands has stimulated development of numerous tourism facilities and infrastructure to meet visitor satisfaction. It is observed in this study that island’s site-plan destination design has contributed to the successful and sustainability of tourism in small island. The key success lies on the successful integration and implementation of three substantial perspectives into practices, namely economic, ecosystem and social perspectives. First, in order to enhance economic benefits, a site-plan design allowing floating cottages establishment to extent room availability, to build strong images as tropical paradise islands, and to enhance tourist satisfaction with the objectives of improving income and sustaining tourist loyalty to the destination. This design is also reducing land risk from tourism impact and it becomes the significant key of second perspective, the ecosystem perspective. Moreover, the ecosystem perspective has been implemented through native vegetation preservation that led island’s wildlife conservation and became potential tourism attraction. The design also develops effective mechanism to manage and regulate visitor flows by establishing visitor track corridors. In implementation, such corridor plays an important role to reduce tourist density in single places and therefore become instrument to reduce severe visitor impact to wildlife, vegetation and heritages of islands. Third, the social aspect of development allowing heritages to conserve and furthermore serve numerous benefits for education, socio-political, culture, and historical studies. Through this study, it is clear that the success of these islands to continuous tourism growth lies on the island’s vision to integrate economic, ecosystem and social perspectives on tourism development.