Abstract Background Despite the fact that the majority of gallstones formed in the gallbladder are mainly composed of cholesterol, as they are formed from cholesterol-supersaturated bile, and hypercholesterolemia is a common metabolic disorder, which is closely related to cardiac, hepatic, renal and other oxidative damage inflammation and necrosis, there is still no consensus regarding the contribution of blood serum lipids in the pathogenesis of gallbladder stone disease (GSD). This study aimed to investigate the relationship between hypercholesterolemia and the risk of new-onset asymptomatic GSD, and to determine the prevalence of factors associated with new-onset asymptomatic GSD in patients with hypercholesterolemia. Methods In this study, 927 Chinese patients with new-onset asymptomatic gallstone disease and 845 healthy controls were enrolled starting from August 2012. Patients were matched for age, gender, race, occupation, systolic blood pressure, diastolic blood pressure, and fasting blood glucose levels (FBG). Body mass index (BMI), nonalcoholic fatty liver disease (NAFLD) and serum lipids indexes were compared and the relationships between BMI, blood lipid and gallbladder stone hazards were examined by logistic multivariate regression models. Results The result showed a significantly higher morbidity with GSD in hypercholesterolemia than non-hypercholesterolemia patients (Χ2 = 17.211, P < 0.001). Of hypercholesterolemia patients, low density lipoprotein (OR = 1.493, P = 0.029) and NAFLD (OR = 2.723, P = 0.022) were significant risk factors for GSD, while being male (OR = 0.244, P = 0.033), weight (OR = 0.961, P = 0.022), high density lipoprotein (OR = 0.305, P < 0.001), and FBG (OR = 0.687, P = 0.034) were significantly negatively correlated with GSD in univariate analysis. Multivariate logistic regression indicated weakly positive correlations with NAFLD (OR = 3.284, P = 0.054), and significant negative correlations with weight (OR = 0.930, P = 0.018), HDL-c (OR = 0.144, P < 0.001), and GSD. Conclusion Hypercholesterolemia acts as an independent risk factor for new-onset asymptomatic GSD, while obesity and NAFLD are synergistic factors. Interestingly, it is first reported that elevated weight was inversely associated with GSD in patients with hypercholesterolemia. The results of this study suggest that effective control of hyperlipidemia is of greater significance than weight loss, which might make the situation worse, in the prevention of GSD in obese patients with hyperlipidemia.