Lipid metabolic disturbance induced by the synthetic steroids used in combination oral contraceptives (COCs) has been considered as one of the potential risk factors of cardiovascular diseases. A lower-dose preparation that contains 20 µg of ethinyl estradiol and 100 µg of levonorgestrel (20EE/LNG) has proven effective in most clinical studies, whereas its effect on lipid metabolism is still unclear. The purpose of this study was to estimate the effect of a lower dose of a COC (containing 20 µg of ethinyl estradiol and 100 µg of levonorgestrel) on lipid metabolism by conducting a systematic review and a meta-analysis. A literature search was performed using MEDLINE (PubMed), Embase, PsycINFO, and the Cochrane Central Register of Controlled Trials (CENTRAL database). The studies that are randomized controlled trials to compare a lower-dose COC (20EE/LNG) with a placebo or another COC that differed in terms of the drug, dosage, regimen, and study length were included. Meanwhile, studies should have evaluated the index of lipid metabolism changes. However, the studies with the interventions fewer than three consecutive cycles or the patients were primarily used the treatment of non-contraceptive were excluded. We pooled the low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), total cholesterol (TC), and triglyceride (TG) results, and compared 20EE/LNG with conventional-dose COCs using fixed-effects meta-analysis with inverse-variance weighting. Five randomized controlled trials, with a total of 423 participants (age range: 18–35 years), were included in this study. The results derived from all the included studies were pooled. LDL-C of 20EE/LNG group showed significant lower than control group after three (SMD, 0.16; 95% CI, 0.03–0.30; <i>P</i>=0.02) and six (SMD, 0.16; 95% CI, 0.01–0.31; <i>P</i>=0.04) cycles of treatment. However, there was no difference between the two groups after 12 cycles of administration (SMD, -0.06; 95% CI, -0.31 to 0.18; <i>P</i>=0.61). The pooled results showed there was a significant increase in HDL-C in the 20EE/LNG group after three cycles of treatment (SMD, 0.43; 95% CI, 0.13–0.73; <i>P</i>=0.005). No significant difference was observed between TC and TG groups. For LDL-C, the low-dose group shows a higher risk of suffering from cardiovascular diseases after three and six cycles of treatment, while no difference is observed after 12 cycles of treatment. For HDL-C, the 20EE/LNG group exhibits favorable effects after three cycles of treatment compared with the control groups. Similar effects are found between TC and TG profiles groups.