Emergy theory and analysis method have been applied in the ecological science and other relative fields. In this paper, Wuyishan national natural reserve in Fujiang province of China is taken as a system, emergy analysis has been used to study its ecotourism situation. The entire value of an ecotourism system can not be completely presented by the traditional method of emergy analysis, therefore, CVM is introduced in order to compensate this, so that a complete value of the system can be presented. In this way, some of new concepts of emergy are proposed such as ideal exchange emergy ratio. The results of this study have been compared with other similar study. This study indicates that: (1) the emergy density of the ecotourism system of Wuyishan natural reserve is 7.31×1011sej/m2, lower than the average of that of Fujian Province(16.62×1011sej/m2), meanwhile the emergy of per person is 2.80×1016sej, higher than that of Fujian Province(5.75×1015sej); the net output of emergy is 3.60,a bit higher than that of the tourist economic system of Yueshi ecological agricultural system in Gongcheng, Guangxi Province(2.79);the ideal exchange ratio of emergy of the ecotourism system of Wuyishan natural reserve is 0.70. (2) The physical environment of Wuyishan national natural reserve has great potential for development; the economy of local community is in the state of underdevelopment, and people′s income is low; the efficiency of productivity of the system is also at low level, with an unbalanced trade with outside; finally, the ecotourism development is just in the state of initiative stage.