Objective To compare the safety and effectiveness of bioabsorbable stents and drug-eluting stents for cardiovascular disease. Methods We searched SinoMed, Wanfang data, Chinese National Knowledge Infrastructure (CNKI), VIP, PubMed, Medline and Embase databases to obtain the clinical trial studies published between Jan. 1980 and Oct. 2018 according to inclusion criteria. The odds ratio (OR) and 95% confidence interval (95% CI) were calculated by the R 3.5.1 software to evaluate the safety and efficacy of bioabsorbable stents and drug-eluting stents in treatment of cardiovascular disease. Results A total of 22 studies with 33 570 subjects were included. Comparing the bioabsorbable stents with the drug-eluting stents, we found that OR (95% CI) for the main safety and effectiveness indicators were as follow:cardiac death (1.01[0.88, 1.16], P>0.05), all-caused death (0.97[0.88, 1.08], P>0.05), myocardial infarction (0.98[0.87, 1.10], P>0.05), target lesion revascularization (0.99[0.89, 1.09], P>0.05), and target vessel revascularization (1.03[0.95, 1.13], P>0.05). The OR (95% CI) was (0.80[0.65, 0.99], P=0.042) for the detection of confirmed or suspected stent thrombosis, (0.97[0.69, 1.37], P=0.906) for early stent thrombus, and (0.61[0.43, 0.86], P=0.004) for late stent thrombus. Conclusion In the treatment of coronary heart disease, the results of this meta-analysis indicate that there are no differences in safety or efficacy between bioabsorbable stents and drug-eluting stents. However, bioabsorbable stents can decrease the risk of stent thrombus, especially for the late stent thrombus.