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Abstract Background The preventive effect of cholesterol efflux capacity (CEC) on the progression of atherosclerotic lesions has been confirmed in animal models, but findings in the population are inconsistent. Therefore, this meta-analysis aimed to systematically investigate the relationship of CEC with coronary artery disease (CAD) and cardiovascular mortality in a general population. Methods Four electronic databases (PubMed, Embase database, Cochrane Library, Web of Science) were searched from inception to February 1st, 2022 for relevant studies, without any language restriction. For continuous variables, the mean and standard deviation (SD), maximum adjusted odds ratios (ORs), relative risks (RRs), or hazard ratios (HRs) and 95% confidence intervals (CIs) were extracted. The random-effects model was adopted to calculate the pooled results, and dose-response analyses were conducted. All pooled results were expressed by standardized mean difference (SMD) and ORs. Results Finally, 18 observational studies were included. Compared with the non-CAD group, the CAD group (SMD -0.48, 95% CI − 0.66 to − 0.30; I2 88.9%) had significantly lower CEC. In the high-CEC population, the risks of CAD (OR 0.52, 95% CI 0.37 to 0.71; I2 81%) significantly decreased, and a linear negative dose-response was detected. However, an association between CEC and the risk of cardiovascular mortality was not found (OR 0.44, 95% CI 0.18 to 1.06; I2 83.2%). Conclusions This meta-analysis suggests that decreased CEC is strongly associated with the risk of CAD, independent of HDL-C level. However, a decreased CEC seems not to be related to cardiovascular mortality. Meanwhile, CEC is linearly negatively correlated with the risk of CAD.