Serum levels of remnant cholesterol have been reported to predict the prognosis of cardiovascular disease, independent of traditional lipid profiles. This study aimed to explore the association between serum remnant cholesterol and the development of nonalcoholic fatty liver disease (NAFLD). A total of 9,184 adults who underwent physical examination annually were included in this study. The association between serum remnant cholesterol and incident NAFLD was analyzed by Cox proportional hazards regression. We evaluated the relative risk of NAFLD in the groups with discordant remnant cholesterol versus traditional lipid profiles using clinically relevant treatment targets. During a total of 31,662 person-years of follow-up, 1,339 incident NAFLD cases were identified. In the multivariable-adjusted model, the fourth quartile of remnant cholesterol was positively associated with NAFLD risks compared with the first quartile (HR: 2.824, 95% CI: 2.268-3.517; P < 0.001). This association remained significant among individuals with normal levels of low-density lipoprotein-cholesterol (LDL-C), high-density lipoprotein-cholesterol (HDL-C) and triglycerides (HR: 1.929, 95% CI: 1.291-2.882; P < 0.001). In individuals achieving the different treatment targets of LDL-C and non-HDL-C for risk stratification according to clinical guidelines, the association between remnant cholesterol and incident NAFLD was still significant. Serum levels of remnant cholesterol have predictive value for the development of NAFLD beyond traditional lipid profiles.