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Dietary fish oil could prevent and treat atherosclerosis by improving lipid metabolism; in apolipoprotein E-deficient (apoE−/−) mice, it was ineffective at lowering serum lipid levels but still showed anti-atherosclerosis action. To date, no direct evidence has comparatively evaluated the effect of docosahexaenoic acid-enriched and eicosapentaenoic acid-enriched phospholipids (DHA-PL and EPA-PL) on atherosclerosis in apoE−/− mice. The present study suggested that both 1% dietary DHA-PL and EPA-PL could significantly reduce atherosclerotic lesions (37.4% and 53.4%, respectively) in high fat diet apoE−/− mice. EPA-PL significantly decreased serum and hepatic lipid levels, by mediating mRNA and protein levels of genes related to hepatic cholesterol metabolism, whereas DHA-PL was ineffective. In the suppression of aortic proinflammatory cytokines, DHA-PL was superior to EPA-PL at reducing TNF-α, IL-6, and IL-1β transcription. In conclusion, the action of DHA-PL was simply anti-inflammatory, and that of EPA-PL was mainly the improvement of lipid metabolism in the amelioration of atherosclerosis.