This study was conducted to assess the effect of eicosapentaenoic acid (20:5n-3, EPA) on lipid accumulation in grass carp Ctenopharyngodon idella adipose tissue both in vitro and in vivo. EPA was observed to inhibit the adipocyte viability in a time and dose-dependent manner. EPA was also found to induce reactive oxygen species accumulation in vitro. The mRNA levels of caspase 3a and caspase 3b, as well as the activity of Caspase 3 increased significantly in vitro and in vivo, whereas the value of B cell leukemia 2-Bcl-2 associated X protein decreased significantly. Besides, the pro-apoptotic effect was relieved by α-tocopherol. Dietary 0.52% EPA had no apparent effect on intraperitoneal fat index. Moreover, EPA promoted the hydrolytic gene expressions in vitro and in vivo, including adipose triglyceride lipase and hormone sensitive lipase-a. Meanwhile, the lipogenic gene expressions of liver X receptor α, sterol regulatory element binding protein-1c and fatty-acid synthase were down-regulated by EPA in vitro and in vivo. However, EPA also acted to promote the marker gene expressions of adipogenesis, including peroxisome proliferator-activated receptor γ and lipoprotein lipase in vitro and in vivo. Contents of EPA increased significantly in the treatment groups in vitro and in vivo. These results support that EPA affects multiple aspects of lipid metabolism, including hydrolysis, lipogenesis, adipogenesis and apoptosis. However, it barely functioned in decreasing the lipid accumulation of Ctenopharyngodon idella under the current culture conditions.