The national parks have management objectives such as ecosystem conservation and sustainable use of natural resources. The realization of these management objectives requires support of a large amount of data and information. Ecological monitoring can help to understand the dynamic change of ecosystems within the national parks and to reveal the impact of management activities, thus providing useful information for the planning and the implementation of management decisions. Since the national park system concept was put forward in 2013, construction of pilot national parks has been gradually carried out in China. Although some of them have achieved monitoring results to some extent by integrating various resources, the pilot national parks still lack in ecological monitoring that can meet management needs in China. To promote the establishment of an ecological monitoring system in national parks of China, we proposed a methodology of constructing an ecological monitoring indicator system in the national parks oriented to management objectives. This methodology consists of five procedures:1) to determine the objectives of ecological monitoring in the national parks. 2) to identify the management objectives of the national parks. 3) to identify key ecological processes in the national parks. 4) to identify the ecological processes that need to be monitored and develop a list of initial monitoring indicators. 5) to determine a list of final monitoring indicators. This methodology was applied in Three-River-Source National Park where management objectives were identified such as ecosystem conservation, maintain sustainable and steady river runoff and key ecological processes were identified at levels of the region, landscape, ecosystem, and population. By matching key ecological processes and management objectives, an ecological monitoring indicator system was established in Three-River-Source National Park, which consists of 93 indicators at two levels. This methodology and its application has laid a foundation for the establishment of an ecological monitoring system in Three-River-Source National Park.