Background: The non-HDL cholesterol to HDL cholesterol (NHDLC/HDLC) ratio is closely related to a variety of dyslipidemia-related disease. This study aimed to inspect the relationship between the NHDLC/HDLC ratio and non-alcoholic fatty liver (NAFLD) in childhood and adolescence. Methods: In this cross-sectional survey, a total of 7,759 eligible Chinese children and adolescents (5,692 boys and 2,067 girls) were received routine medical examinations. The anthropometric and laboratory data of the subjects were collected. NAFLD was diagnosed by liver ultrasonography. The binary logistics regression analysis was performed on NHDLC/HDLC ratio, NHDLC and HDLC and NAFLD. ROC curve analysis was exploited to compare the diagnostic significance of the above parameters for NAFLD. Results: The total prevalence of NAFLD was 4.36%, and the prevalence of boys was higher than that of girls (5.61% vs. 1.9%, P < 0.001). The prevalence of NAFLD was positively correlated with the NHDLC/HDLC ratio (P < 0.001). The binary logistics regression analysis demonstrated that the OR was 8.61 (95% CI, 5.90-12.57, P < 0.001) in the tertile 3 (highest NHDLC/HDLC ratio) compared with the tertile 1 (lowest NHDLC/HDLC ratio). When potential confounders (age, sex, BMI, ALT, UA, TB, FPG and HOMA-IR) were adjusted, the OR for the tertile3 (OR=1.83, 95% CI, 1.04-3.22, P = 0.035) was still drastically higher than that of the tertile 1. The AUC of the NHDLC/HDLC ratio of boys was 0.787, which was significantly greater than that of NHDLC and HDLC (0.719 and 0.726, P < 0.001). For girls, the AUC of NHDLC/ HDLC ratio was 0.763, which was also significantly greater than that of NHDLC (0.661, P < 0.001). Furthermore, the cutoff points of NHDLC/HDLC ratio were 2.475 in boys and 2.695 in girls. Conclusions: The NHDLC/HDLC ratio was positively correlated with NALFD in Chinese children and adolescents. It may serve as an effective indicator to help identify NALFD in children and adolescents.