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Long-chain <i>n</i>-3 polyunsaturated fatty acid (PUFA) supplementation has shown potential benefits in the prevention of coronary heart disease (CHD); however, the impact of omega-3 fatty acid levels on CHD risk remains a subject of debate. Here, we aimed to investigate the association between <i>n</i>-3 PUFA levels and the risk of CHD, with particular reference to the subtypes of <i>n</i>-3 PUFA. Methods: Prospective studies and retrospective case-control studies analyzing <i>n</i>-3 PUFA levels in CHD, published up to 30 July 2022, were selected. A random effects meta-analysis was used for pooled assessment, with relative risks (RRs) expressed as 95% confidence intervals (CIs) and standardized mean differences expressed as weight mean differences (WMDs). Subgroup and meta-regression analyses were conducted to assess the impact of <i>n</i>-3 PUFA exposure interval on the CHD subtype variables of the study. Results: We included 20 prospective studies (cohort and nested case-control) and 16 retrospective case-control studies, in which <i>n</i>-3 PUFAs were measured. Higher levels of <i>n</i>-3 PUFAs (ALA, EPA, DPA, DHA, EPA + DHA, total <i>n</i>-3 PUFAs) were associated with a reduced risk of CHD, with RRs (95% CI) of 0.89 (0.81, 0.98), 0.83 (0.72, 0.96); 0.80 (0.67,0.95), 0.75 (0.64, 0.87), 0.83 (0.73, 0.95), and 0.80 (0.70, 0.93), respectively, <i>p</i> < 0.05. CHD patients had significantly lower <i>n</i>-3 PUFA levels compared to healthy controls (<i>p</i> < 0.05). In the subgroup analysis, a significant inverse trend was found for both fatal CHD and non-fatal CHD with <i>n</i>-3 PUFA (EPA + DHA) levels. Also, the link between <i>n</i>-3 PUFA levels in erythrocytes with total CHD was generally stronger than other lipid pools. Conclusions: <i>n</i>-3 PUFAs are significantly related to CHD risk, and these findings support the beneficial effects of <i>n</i>-3 PUFAs on CHD.