Komodo National Park (KNP) has prioritized eight out of 20 existing ecosystem services. KNP follows the concept of conservation and educational tourism, where visitors can see wildlife and enjoy panoramic views. The negative impact of increasing visitor numbers is the reduction of ecosystem value and benefits. In this article, the expert-based in-depth discussion method is presented, which is complemented by the interpretive structural modelling and system dynamics method. In the weighting phase, the Analytical Hierarchy Process (AHP) and spatial analysis using the Geographic Information System (GIS) and a market valuation of ecosystem service benefits are used. The results of the analysis show that the lost value of ecosystem services will reach USD 727 million, while it will be USD 661 thousand if the number of visitors is limited. This value is considered feasible to achieve restoration while providing economic and sustainable benefits. The programme to increase the number of visitors must be integrated with the management of tourist attractions on other islands in Komodo National Park, Labuan Bajo, and West Manggarai by extending the length of visitors’ stay.