Previous randomized controlled trials (RCTs) made direct comparisons between EPA/DHA versus ALA on improving cardiovascular risk factors and have reached inconsistent findings. The aim of this meta-analysis was to compare the effects of EPA/DHA vs. ALA supplementation on cardiometabolic disturbances. Databases including MEDLINE, Embase, PubMed and Cochrane Trials were searched until December 2019. The pooled effects (weighted mean difference, WMD) of outcomes with moderate and high heterogeneity were calculated with a random-effects model, while low heterogeneity was calculated with a fixed-effect model. Fourteen RCTs with 1137 participants who met the eligibility criteria were pooled. Compared with participants supplemented with ALA, those who received EPA/DHA supplementation experienced a greater reduction in triglycerides (TG) (WMD −0.191 mmol l −1 ; 95% CI −0.249, −0.133) but a greater increase in high-density lipoprotein (HDL) (WMD 0.033 mmol l −1 ; 95% CI 0.004, 0.062), low-density lipoprotein (LDL) (WMD 0.130 mmol l −1 ; 95% CI 0.006, 0.253) and total cholesterol (TC) (WMD 0.179 mmol l −1 ; 95% CI 0.006, 0.352). In subgroup analyses, the WMD for TG was much lower in trials with participants >40 years old (−0.246 mmol l −1 ; 95% CI −0.325, −0.167). When DHA and EPA were separately administered, modest increases in HDL were observed in trials that used DHA as a supplement (0.161 mmol l −1 ; 95% CI 0.017, 0.304), but not in trials using EPA (0.040 mmol l −1 ; 95% CI −0.132, 0.212). In conclusion, dietary EPA/DHA supplementation improved the TG and HDL status but increased LDL levels in comparison with ALA.