By analyzing the internal factors of eco-tourism destination marketing system, this article constructs 29 influence indexes and establishes marketing system evaluation index system of eco-tourism destination in terms of variance method based on analytic hierarchy process. Based on the analysis and evaluation of the experts about the 8 counties in Three Gorges reservoir, the eco-tourism destination marketing system of Wulong and Badong are regarded as the best, and the weaknesses of the system in the those districts and counties are also discovered, which will offer some advice for the future development.