Objective To explore the method to carry out epidemiological investigation of chronic kidney disease (CKD) in rural area surrounding the Tarim Basin, and to elucidate the prevalence and risk factors associated with CKD among the Uygur adults in Moyu county. Methods A total of 1650 residents (age >18 years) from 15 villages in 3 rural town of Moyu county were randomly selected by using a stratified, multistage sampling. All the residents were interviewed and received physical examination and tested for random spot urine of albumin to creatinine ratio (ACR). Estimated glomerular filtration rate (eGFR) was calculated by modified factors of CKD were examined. Results Valid data of 1552 subjects were enrolled in the study. After the adjustment of age and gender component, the prevalence of albuminuria and reduced eGFR was 4.5% (95% CI 4.4-4.6) and 1.4% (95% CI 1.4-1.5) respectively. Approximately 5.4% subjects had at least one indicator of kidney damage. Age and hypertension were independently associated with CKD. Conclusions Experience and method of epidemiology investigation of CKD in the rural areas of Uygur are obtained through this study. The prevalence of CKD is 5.4% and the awareness is 12.5% in the Uygur adults of Moyu county. Independent risk factors associated with CKD are hypertension and age.