Background Gallstone disease (GSD) is a common and costly biliary disorder. Multiple studies have investigated the associations between blood lipid metabolism and GSD risk; however, the results are inconsistent. This research aimed to comprehensively evaluate the relationships among serum total cholesterol, low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, triglycerides and GSD risk. Methods Firstly, a multi-center cross-sectional study was carried out. Subjects who participated in the health examination in three hospitals between January 2015 and May 2020 were recruited. Multivariable logistic regression was used to investigate blood lipid metabolism associated with GSD risk. Then, a meta-analysis was performed to verify the associations further. Medline and Embase databases were systematically searched before June 10, 2021. The DerSimonian and Laird random-effect model was utilized when the heterogeneity was high; otherwise, fixed-effect model was adopted. Results There were 548,934 eligible participants included in the multi-center study, and 45,392 of them were diagnosed with GSD. The results demonstrated that total cholesterol and HDL cholesterol were negatively associated with GSD risk in both high vs. low model and per mmol/L increase model, while triglyceride was positively associated with GSD risk in the per unit increase model. In the meta-analysis, 104 studies with approximately 3 million participants were finally included. The results verified that HDL cholesterol [odds ratio (OR) = 0.636, P = 5.97 x 10(- 16) in high vs low model; OR = 0.974, P = 6.07 x 10(- 05) in per unit model] and triglyceride (OR = 1.192, P = 3.47 x 10(- 05) in high vs. low model; OR = 1.011, P = 5.12 x 10(- 05) in per unit model) were related to GSD risk in the two models. Conclusions The findings indicated that low HDL cholesterol levels and high triglyceride levels were risk factors for GSD. This study provides a basis for identifying the population at high risk for GSD and implementing tertiary prevention strategies for GSD, thus contributing to GSD prevention as well as disease burden relief.