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. •Genotype was the major contributor to the total variation in antioxidant factor activity .•The strongest ability to distinguish the three antioxidant factors was detected at 16 °C.•The five test temperatures were divided into two regions, 16–20ºC region and 24–32ºC region.•SOD exhibited the best activity and stability of the three antioxidants at the five temperatures tested.