Nature reserves are key sites for ecotourism. In the context of sustainable development, a great number of ecotourism practices have been carried out in nature reserves around the world. Important ecotourism practices in nature reserves include the establishment of ecotourism certification systems, the development of management mechanisms promoting effective community participation and the development of standards for ecotourism practices. This paper uses questionnaires, a field investigation and interviews to examine the obstacles influencing the sustainable development of ecotourism in nature reserves, taking three nature reserves in Liaoning Province to serve as examples. The study found that there are two kinds of obstacles to the sustainable development of ecotourism in nature reserves. The first group of obstacles all represent common problems in China including: (1) environmental education is ignored; (2) community participation occurs on an ad hoc basis; (3) tourism management is not rigorous; (4) nature reserve administration is in a state of confrontation with local governments and residents. The second group of obstacles consists of specific problems faced by ecotourism in the three nature reserve, each of which has its own natural, social, cultural and economic environment that generate unique difficulties for ecotourism. In order to promote the healthy improvement of nature reserve ecotourism and achieve the goal of sustainable development, the research team puts forward five suggestions, developing correct understanding, striving to meet the reasonable demands of stakeholders, establishing scientific mechanisms, increasing the social responsibility of management departments of nature reserve ecotourism, and providing separate supervision and management.