Cynomorium songaricum is a nationally protected plant in China, and appears on a list of species accorded “second-class” protection. C. songaricum is esteemed for its high medicinal value, and thrives in ecologically fragile desert regions. In recent years, climate change has posed a significant threat to the geographical distribution of C. songaricum. This study aimed to clarify the main environmental factors affecting the distribution of C. songaricum in China and to emphasize the significance of identifying potential suitable areas for effective protection and management. Based on 166 valid distribution records and 39 natural environmental variables, this study employed the maximum entropy model (MaxEnt) to simulate the potential geographical distribution of C. songaricum along two representative climate change projection pathways (SSP126 and SSP585) for both the current period and future scenarios (2050s and 2070s). The study explored the most critical environmental factors affecting C. songaricum distribution and predicted the spatial distribution pattern of suitable habitat areas in response to climate change. The knife-cut method was employed to assess the contribution rate of environmental variables to the model, helping to identify the primary factors influencing the distribution of C. songaricum. The model’s prediction results indicated that the currently simulated potential distribution area of C. songaricum closely aligns with its actual distribution. The area under the receiver operating characteristic curve (AUC value) was 0.900, indicating strong predictive performance. The results indicate that precipitation in the wettest month and average temperature during the coldest season are critical variables determining the habitat of C. songaricum. These two criteria are followed in importance by basic soil saturation, altitude, the highest temperature in the warmest month and precipitation in the driest season, in that order. Future climate change is expected to narrow the habitat of C. songaricum and shift its distribution eastward. The predictions of potential suitable habitat areas for C. songaricum in this study can provide guidelines for its protection and management.