Based on 62 natural distribution points and 15 environmental factors, we analyzed and predicted the potentially suitable areas, driving factors, and ecological niche parameters determining the distribution of Fritillaria walujewii under the reference climate of 1961-1990 and under the predicted climate of 2050 (2041-2060). We based our predictions on RCP2.6 and RCP6.0 scenarios using ArcGIS and the maximum entropy (MAXENT) model. The major results were as follows:(1) under the reference climate, the potentially suitable areas for F. walujewii were mainly restricted to the Altai region, western and southern Junggar Basin, southwestern Alashankou, southern Ili River Valley, and western Turpan Basin. Specifically, the most suitable areas were concentrated in southwestern Junggar Basin, Tacheng, and the middle and southern Ili River Valley; (2) the potential distribution of F. walujewii in 2050, based on two climate scenarios and compared with the reference climate, will possibly decrease by about 0.94% and 0.23%. The new potential habitats would mainly distributed in the western Junggar Basin. However, the most suitable distributions for F. walujewii are predicted to become slightly smaller (by about 0.42% and 0.39%) in the middle and southern Ili River Valley and Tacheng; (3) annual precipitation, precipitation in the driest month, mean temperature in the driest quarter, and altitude were the main limiting factors affecting distribution of F. walujewii; the total cumulative contribution of these factors was 88.58%. Ecological niche parameters that determine the most suitable areas under the reference climate were:an annual precipitation of 248-469 mm, precipitation in the driest month of 3-19 mm, mean temperature in the driest quarter of -22.7 to -2.0℃, and altitude of 1350-2100 m.