The spleen is an important organ in the immune function of fish, and it is also important for hematogenesis and antibody and granulocyte production. However, the effect of oxidized fish oil on the spleen of hybrid grouper (♀ Epinephelus fuscoguttatus × ♂ Epinephelus lanceolatus) is unknown. In this study, hybrid groupers were fed with oxidized fish oil and the spleen index, antioxidant ability, histology and transcriptome were investigated. Oxidized fish oil did not affect the spleen index. Levels of superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GSH-Px) and malondialdehyde (MDA) in the spleen were significantly increased as the amount of oxidized fish oil in the diet increased, but the vitamin E concentration was significantly decreased. The morphological organization of the spleen was damaged with increased oxidative stress. And the spleen reacted to oxidative stress by platelet activation, FOXO and notch signaling pathways, which involved amyloid beta precursor protein binding family B member 1 interacting protein (APBB1IP) gene, glucose-6-phosphatase (G6PC) gene, histone acetyltransferase p300 (EP300) gene, insulin gene and notch 2 gene. In conclusion, the oxidized fish oil caused oxidative stress and damaged its structure. Additionally, oxidized fish oil changed the transcription profile of the spleen.