Background Rising costs of medical service and the need to better utilize limited resources makes the pursuit of hospital efficiency a key objective for healthcare systems. There is inconsistent evidence regarding the comparison of hospital efficiency. In China, limited research has been conducted in comparing the efficiency of Chinese public and private hospitals at the county-level, especially in western China where national GDP falls in the lowest quartile. Method We selected county-level hospitals from one western province by convenience sampling and conducted questionnaire survey in 2018. We first measured efficiency for the hospitals by bootstrap data envelopment analysis (DEA) with the following input variables: hospital bed, expensive equipment, medical staff and operating expenditure, and output variables revenue from outpatient and inpatient services; the efficiency scores were compared statistically between public and private hospitals by normality and non-parametric tests. Then we conducted bootstrap truncated regression on the estimated efficiency scores against environmental and institutional factors. Results Sixty-four county hospitals from 30 counties across the province were included in the study: 52 public hospitals, and 12 private hospitals. Relative efficiency was estimated to be 0.83 for public hospitals, and 0.96 for private hospitals, with statistically significant difference (p=0.001). Approximately 25.0% and 83.3% of public and private hospitals, respectively, were efficient. The truncated regression showed that being a private hospital (p<0.001), higher physician-nurse ratio (p=0.007), and higher revenue from outpatient services (p=0.041) were able to increase the efficiency by 0.158 (0.116, 0.199), 0.305 (0.190, 0.420), and 0.253 (0.129, 0.378), respectively. Conclusion The overall efficiency of the county level hospitals in a western province of China in 2018 was low. Private county hospitals were significantly more efficient than their public counterparts. Outpatient service revenue and physician nurse ratio were determinants of county hospital efficiency and may serve as future policy intervention targets.