Atherosclerosis (AS) caused by a high-fat diet becomes a critical cause of cardiovascular diseases, which has been regarded as an urgent public health problem. Omega-3 polyunsaturated fatty acids (omega-3 PUFAs) have many beneficial effects on human health. However, in recent years, the critical role of gut microbiota in atherosclerosis has been gradually proposed, and the impact of omega-3 PUFAs on cardiovascular diseases via gut microbiota in rabbits remains unknown. Likewise, the role of omega-3 PUFAs in regulating endothelial lesions, visceral injury, and vascular inflammation caused by high-fat diet-induced trimethylamine-nitrogen oxide (TMAO) has not been reported. Here, we investigated the effects of omega-3 PUFAs administered orally on atherosclerosis via an atherosclerotic rabbit model induced by a high-fat diet. The results showed that omega-3 PUFAs obtained from deep-sea fish oil can alleviate high-fat diet-induced atherosclerosis by inhibiting the increase of plasma TMAO and the formation of liver foam cells, reducing inflammatory factors, fat deposition, and plasma lipid levels and suppressing organ damage. Furthermore, gut microbiota disrupted by a high-fat diet were remodeled in rabbits treated with omega-3 PUFAs. These results further confirm that omega-3 PUFAs are promising nutritional and medical health foods that can be supplemented daily to prevent cardiovascular diseases.