The Fritillaria species has become rare due to excessive harvesting, and thus identifying new ecological distribution of Fritillaria species and predicting its response to climate change are necessary for plant conservation and cultivation. In this study, areas with potential ecological suitability for Fritillaria delavayi, Fritillaria taipaiensis, and Fritillaria wabuensis were predicted using Biomod2 according to current occurrence records and bioclimatic variables. Temperature seasonality was the most important environmental variable for Fritillaria taipaiensis and Fritillaria wabuensis, while isothermality was most important for Fritillaria delavayi. The current suitable areas for three Fritillaria species were found to be distributed in south-west China, accounting for approximately 17.72%, 23.06% and 20.60% of the total area of China, respectively. During the highest concentration of greenhouse gas emission (SSP585), the suitable habitats of F. delavayi and F. wabuensis reached the maximum from 2021 to 2100, while that of F. taipaiensis reached the maximum from 2021 to 2100 during low emission (SSP126). The niche overlap of three Fritillaria species was found to be significantly related to the clustering tree based on chemical composition (P≤0.05), while no correlation was observed between niche overlap and DNA phylogenies, indicating that spatial distribution had a major influence on chemical composition in the Fritillaria species. Species-specific habitats were also predicted in order to decrease habitat competition. Overall, the findings of this study may offer new insight into the potential distribution and ecological niche of the three species for future conservation and management.