Climatic variables are important conditions for plant growth, development and reproduction. Citrus medica L. var. sarcodactylis Swingle (Rutaceae: Citrus) is one of the traditional bulk Chinese medicinal materials in China with the effects of bacteriostasis, anti-inflammatory, anti-oxidation, anti-cancer cells, regulating the immun. Analyzing the impact of climate change on geographical distribution of C. medica L. var. sarcodactylis can provide strong support for its production layout and agricultural zoning. In our paper, MaxEnt and ArcGIS were applied to simulate the suitable areas of C. medica L. var. sarcodactylis in China from the perspectives of bioclimate, soil, topographic factors and human activities, and the future climate scenarios generated by global climate models (GCMs) were selected to predict its suitable areas in 2050s and 2090s. Results showed that, 1) Under current climate condition, areas of the total, most, moderately and poorly suitable habitats of C. medica L. var. sarcodactylis in China were 177.36×104 km2, 22.27×104 km2, 51.96×104 km2 and 103.13×104 km2 respectively. The range of the most suitable habitat was the narrowest, which was located in the middle east of Sichuan, western Chongqing in the upstream of the Yangtze River Basin, southern Guizhou and western Guangxi in the upstream of the Pearl River Basin, central and southern Yunnan and Southeast Tibet in the Middle-Lower reaches of the Southwest River Basin and western Taiwan. 2) Under the future climate change scenarios, the total suitable area showed a significant increase trend in 2090s, and the change of most, moderately and poorly suitable habitats showed no obvious law. 3) Under SSP1-2.6, SSP2-4.5 and SSP5-8.5 scenarios, the centroid of the most suitable habitat of C. medica L. var. sarcodactylis would move to the northwest, southeast and southwest respectively.