Purpose: China’s Ministry of Health has enacted Rural Primary Health Care Program (2001–2010) (HCP) guidelines to improve the quality of people’s health. However, the program’s success in Western China remains unevaluated. Thus, this study aims to begin to fill that gap by analyzing the provision and utilization of Rural Primary Health Care (RPHC) in Western China. Methods: A cross-sectional study was conducted to collect secondary data on the socio-economic characteristics, system construction, services use and implementation of RPHC, and the residents’ health status of the sampled areas. Four hundred counties from 31 provinces in China were selected via stratified random sampling, including 171 counties from 12 Western provinces. Twenty-seven analysis indicators, covering system construction, services use and implementation of RPHC were chosen to assess Western China’s primary health quality. Analysis of Variance (ANOVA) and Least Significant Difference (LSD) methods were used to measure the RPHC disparities between Western and Eastern and Central China. Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) was used to rank Western, Eastern and Central internal provinces regarding quality of their RPHC. Results: Of the 27 indicators, 13 (48.15%) were below the standard in Western China. These focused on rural health service system construction, Chinese medicine services, and public health. In the comparison between Western, Central and Eastern China, 12 indicators had statistical significance (p < 0.05), and using LSD to compare between Western and Eastern China, all indicators were statistically significant (p < 0.05), demonstrating regional disparities. Xinjiang Province’s RPHC ranked highest overall, and Yunnan Province ranked the lowest, indicating the internal differences within the 12 Western provinces; and Western provinces’ Ci value was lower than that of Eastern and Central China overall. Conclusion: Western China’s RPHC has proceeded well, but remains weaker than that of Eastern and Central China. Differences within Western internal provinces threaten the successful implementation of RPHC.