In order to increase the number of tourism in ecotourism, enhance the ecotourism attractions. It is essential to construct the ecotourism service system for the Penghu National Scenic Area because the ecology system is sensitive and frangible. This study adopts the Fuzzy Delphi method and Analytic Hierarchy Process (AHP) to establish an index framework of ecotourism service system of Penghu National Scenic Area. The results indicated that there are 4 dimensions which include 21 factors service attributes are identified as the service system for traveling. The findings are concluded as follows:(1)the security management capability is the main principle for ecotourism service system;(2)the ecological diversity is fundamental for the marine environment and the core resource for ecotourism;(3)the transportation capacity and environmental quality need to improve; (4)the marine environmental resources is the most important item for sound ecotourism development; (5)the enhancement of the operation willingness of local communities can promote ecotourism development;(6)the natural resources should be protected to provide an ideal recreational environment for ecotourism;(7)the development of ecotourism needs to support local conservation to achieve sustainability. The perspectives of sustainability and service system are involved to support the value of this study, which can continuously sustain Penghu archipelago.