In this study, using Cathaya argyrophylla Chun et Kuang based on 65 current geographical distribution records, and 19 bioclimatic factors based on maximum entropy models (MaxEnt), we estimated the transformation of the potential geographic distribution and habitat fragmentation of C. argyrophylla for the 2050s and 2070s under the climate change scenarios of RCP 2.6, RCP 4.5, RCP 6.0, and RCP 8.5 emission scenarios. The results showed that in the current climate conditions, the suitable habitat area of C. argyrophylla accounted for about 14.32% of the research area, and was mainly distributed at 24°-32°N and 105°-114°E, located Southeast of the Sichuan Basin, Northeast of the Yunnan-Guizhou Plateau, West of Nanling, and North of the Zhejiang-Fujian hilly region. Under the future climate scenarios, the characteristics of suitable habitat change of C. argyrophylla were obvious, and mainly manifested in increased suitable habitat areas and aggregations. Results of the landscape index and habitat fragmentation of suitable habitat for C. argyrophylla showed that climate change would lead to increased patches, patch density, and area weighted mean shape index, with less influence on the landscape division and aggregation indexes. Simultaneously, the effect of climate change on habitat fragmentation of C. argyrophylla mainly reflected on the weakening of the polarization phenomenon of habitat fragmentation, and higher overall fragmentation. In this research, seven indicators of the quantitative comprehensive analysis were more indicative than single indexes or multiple indicators of qualitative analysis, and were more representative of actual C. argyrophylla habitat fragmentation.