Objective: To analyze the association between fat mass percentage (FMP) and waist circumference (WC) with cardiovascular risk factors in children and adolescents in Yinchuan City, and to provide a reference for preventing and contyolling the risk factors of cardiovascular diseases among children and adolescents. Methods: A questionnaire survey, physical examination, body composition determination and biochemical tests were conducted among 1 043 children aged 12-18 years in Yinchuan selected through a convenient cluster sampling method. Results: Among boys and girls, both FMP and WC were associated with high rate of high blood pressure and high TG in children and adolescents(P<0.01). The increased risk of metabolic abnormalities by FMP and WC were 1.14-2.36 times and 1.32-2.09 times, respectively. About 4.9%-22.1% of cardiovascular disease risk was explained by the combination of FMP and WC, which was significantly higher than separate interpretation of FMP or WC (3.5%-22.0%). Standardized regression coefficient for TC and LDL-C (0.25 and 0.22) was greater than WC (0.17 and 0.14) by FMP, and the absolute value of the standardized regression coefficient for SBP, DBP, TG, HDL-C was less than WC by FMP. The predictive risk for high blood pressure, high TG, high TC, low HDL-C and high LDL-C by combination of FMP and WC was 3.67(95%CI=2.42-556), 3.09(95%CI=2.04-4.69), 3.37(95%CI=1.38-8.28), 2.00(95%CI=1.35-2.98) and 4.73(95%CI=2.15-10.44) times higher than different combinations risk groups(P<0.01). Conclusion The ability of fat mass percentage and waist circumference to predict the risk of cardiovascular risk factors is similar. It might be used as a predictor of cardiovascular risk factors in children and adolescents. It is recommended to combine FMP with WC to predict the risk of cardiovascular disease among children and adolescents.