Objectives Non-communicable diseases, which can refer to chronic diseases that are not caused by infectious agents and can endure for a long time, are currently regarded as a critical public health problem in China. This study aimed to estimate the prevalences of self-reported physician-diagnosed chronic diseases among urban and rural populations aged 15 years and older in Shaanxi Province, China, during 2003−2013 and explore how these changes differ by subpopulation. Methods Three independent cross-sectional surveys were implemented in 2003, 2008 and 2013 in Shaanxi Province. A multistage stratified cluster random sampling method was used in each wave to collect representative samples. In total, 10,568 residents in 2003, 15,453 in 2008 and 48,808 in 2013 were included in this analysis. Information on self-reported physician-diagnosed chronic diseases was collected using face-to-face interviews in each survey. Multilevel Poisson regression with robust error variance was employed to calculate the adjusted prevalence ratios to estimate the relative change in chronic conditions in 2008 and 2013, compared to that in 2003. Results In 2013, 23.9%/22.1% of urban/rural residents, respectively, reported having at least one chronic condition, which represents an increase from 17.0%/15.1%, respectively, in 2008 and 12.8%/10.9%, respectively, in 2003. Adjusted for socio-demographic characteristics, the prevalence of chronic diseases was significantly higher in 2013 than that in 2003. Among the chronic diseases studied, the prevalence of hypertension and diabetes has increased dramatically over a decade. The increase in chronic diseases occurred mainly among the middle-aged and elderly. Conclusions Chronic diseases are highly prevalent and continuously increasing in the adult population in Shaanxi Province from 2003 to 2013. Given its large aging population, China may face a greater chronic disease burden. A national chronic disease surveillance system and screening program should be established to acquire comprehensive information regarding the distribution and trends of chronic diseases.