Non-high-density lipoprotein cholesterol (non-HDL-C) may be equivalent to or superior to low-density lipoprotein cholesterol (LDL-C) for the prediction of cardiovascular disease (CVD). However, studies comparing the predictive values of LDL-C and non-HDL-C levels for CVD have yielded conflicting results. In this study, we evaluated the relationship between non-HDL-C, LDL-C, and CVD using a large-scale population dataset from the National Health Information Database (NHID). We performed a retrospective observational cohort study of 3,866,366 individuals ≥ 20 years, from 2009 to 2018, using the NHID. The participants were divided into LDL-C and non-HDL-C quartiles. The outcome variables included stroke, myocardial infarction (MI), and both. All outcomes were analyzed using Cox proportional hazards regression analysis while controlling for baseline covariates (age, sex, smoking, drinking, regular exercise, body mass index, diabetes, hypertension, and statin use). During 9.1 years of mean follow-up, stroke was diagnosed in 60,081 (1.55%), MI in 31,234 (0.81%), and both stroke and MI in 88,513 (2.29%) participants. Multivariate-adjusted hazard ratios (HRs) for patients in the highest non-HDL-C quartile demonstrated that these patients had a higher risk of stroke (HR, 1.254; 95% confidence interval [CI], 1.224-1.285), MI (HR, 1.918; 95% CI, 1.853-1.986), and both (HR, 1.456; 95% CI, 1.427-1.486) compared with participants in the lowest quartile. These were higher than the HRs for patients in the highest LDL-C quartile for stroke (HR, 1.134; 95% CI, 1.108-1.160), MI (HR, 1.601; 95% CI, 1.551-1.653), and both (HR, 1.281; 95% CI, 1.257-1.306). In our large population study, higher non-HDL-C levels were associated with CVD than LDL-C levels.