There may be differences in optimal anthropometric cut-offs for diagnosing obesity among different regions of China. However, there has been little studies about choosing effective obesity indicators in Han People of low-income Chinese adults in southwest China. The purpose of this study was to compare and evaluate the associations between different obesity indicators and cardiovascular disease risk factors (CVDRF) and choose the optimal cut-off values.A cross-sectional study was carried out in southwest of China, with multi-stage sampling enrolling 2112 subjects aged 20 to 80 years old. Anthropometric measurements included Body mass index (BMI), waist circumference (WC), Hip circumference, waist-to-hip ratio (WHR), and waist-to-height ratio (WHtR). We measured the percentage of body fat (PBF) by bioelectrical impedance analyzer to assess the body composition. The validity of different obesity indicators in assessing CVDRF risk were assessed through comparison area under curve of different indicators in assessing CVDRF risk in different gender. Logistic regression models were used to evaluate the association between the obesity indicators and CVDRF.When both male and female were considered, the optimal indicators were WHtR and percentage of body fat PBF for hypertension, WHR and WHtR for dyslipidemia. Both WC and WHtR were optimal indicators in assessing metabolic syndrome risk for both genders. When both disease and gender were considered, WHtR was the best associated indicators with various CVDRF. The cut-off of BMI and WC were consistent to the definition of obesity in Working Group of China. The WHtR positively correlated with the CVDRF. The cut-off of WHtR to do what was approximately 0.50 for adults in both genders in southwest of China.WHtR may be the best associated indicators for obesity-related CVDRF among the others (BMI, WC, Hip circumference, PBF, and WHR) in southwest of China. The cut-off of WHtR was approximately 0.50 for adults in both genders in southwest of China.