The activities of antioxidant factors superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPX) were measured in the livers of Takifugu rubripes cultured at 16 °C, 20 °C, 24 °C, 28 °C, and 32 °C. Additive main effects and multiplicative interaction (AMMI) and genotype main effects and genotype × environment interaction (GGE) Biplot analyses were used to analyze the effects of genotype × temperature interactions on the antioxidant activities. The results of AMMI analysis revealed that antioxidant activities were significantly affected by genotype (93.532%), temperature (2.978%), and genotype × temperature (2.026%) interactions. GGE Biplot analysis revealed differences in the ranking of the three antioxidant activities at the five culture temperatures: the strongest ability to distinguish the three antioxidant factors was detected at 16 °C; the five test temperatures were divided into two regions, 16–20 °C and 24–32 °C; the activity of SOD was highest at 16–20 °C and GPX activity was highest at 24–32 °C; SOD exhibited the best activity and stability of the three antioxidants at the five temperatures tested.