Objective: To analyze specific differences between urban and rural areas in government health expenditures in western China, and provide evidence support for the rational investment of regional and urban-rural medical and health expenditures by the governments in western China. Methods: Based on the panel data of 132 cities in 12 provinces in western China from 2009 to 2019 , the fixed effect model and the threshold effect model are used to empirically analyze the factors that affect government health expenditure. Results: Per capita GDP and rural residents' income are the main factors affecting government health expenditures. The per capita GDP thresholds were 9.84 and 10.48, the urban residents' income thresholds were 9.73 and 10.13, and the rural residents' income thresholds were 8.67 and 9.22. Government health expenditures in western China are more skewed towards urban residents in economically developed areas and rural residents in low-income groups. Conclusion: There are significant differences in government health expenditures among different regions and between urban and rural areas in western China. Promoting the coordinated and balanced development of regional and urban and rural medical and health care needs to be carried out according to local conditions and step by step.