Background: Low-density lipoprotein cholesterol (LDL-C) always underestimates the true cholesterol burden in patients with nonalcoholic fatty liver disease (NAFLD). We aimed to compare LDL-C and non-high-density lipoprotein cholesterol (non-HDL-C) in the identification of high-risk dyslipidemic phenotypes in those with NAFLD. Methods: We conducted a cross-sectional analysis using a cohort of 9560 apparently healthy Chinese adults who underwent comprehensive health checkups including abdominal ultrasonography. Results: Among 3709 patients with NAFLD, the prevalence of abnormal LDL using LDL-C was 68.5%, whereas the prevalence was relatively lower when using non-HDL-C (55.9%). The concordance between non-HDL-C- and LDL-C-based diagnoses of abnormal LDL was similar in the hypertriglyceridemic (kappa = 0.56; 95% CI 0.52-0.60) and normotriglyceridemic subgroups (kappa = 0.47; 95% CI 0.44-0.51). Non-HDL-C detected fewer patients with abnormal LDL than LDL-C in normotriglyceridemic patients. However, non-HDL-C detected more patients with abnormal LDL than LDL-C in hypertriglyceridemic patients: 114 of the 1662 patients considered as abnormal LDL according to LDL-C fell into the normonon-HDL-C phenotype, whereas 204 of the 1662 patients considered as abnormal LDL according to non-HDL-C fell into the normoLDL-C phenotype. Conclusion: Among patients with NAFLD, LDL-C is superior to non-HDL-C in the detection of high-risk phenotypes in normotriglyceridemic patients, whereas non-HDL-C seems to be superior in hypertriglyceridemic patients.