The United Nations’ expanded program for Reducing Emissions from Deforestation and Forest Degradation (REDD+) aims to mobilize capital from developed countries in order to reduce emissions from these sources while enhancing the removal of greenhouse gases (GHGs) by forests. To achieve this goal, an agreement between the Parties on reference levels (RLs) is critical. RLs have profound implications for the effectiveness of the program, its cost efficiency, and the distribution of REDD+ financing among countries. In this paper, we introduce a methodological framework for setting RLs for REDD+ applications in tropical forests in Xishuangbanna, China, by coupling the Good Practice Guidance on Land Use, Land Use Change, and Forestry of the Intergovernmental Panel on Climate Change and land use scenario modeling. We used two methods to verify the accuracy for the reliability of land classification. Firstly the accuracy reached 84.43%, 85.35%, and 82.68% in 1990, 2000, and 2010, respectively, based on high spatial resolution image by building a hybrid matrix. Then especially, the 2010 Globeland30 data was used as the standard to verify the forest land accuracy and the extraction accuracy reached 86.92% and 83.66% for area and location, respectively. Based on the historical land use maps, we identified that rubber plantations are the main contributor to forest loss in the region. Furthermore, in the business-as-usual scenario for the RLs, Xishuangbanna will lose 158,535 ha (158,535 × 104 m2) of forest area in next 20 years, resulting in approximately 0.23 million t (0.23 × 109 kg) CO2e emissions per year. Our framework can potentially increase the effectiveness of the REDD+ program in Xishuangbanna by accounting for a wider range of forest-controlled GHGs.