In fish, the development of the spleen is not as perfect as that of higher vertebrates, but it has the same functions that the spleen should have. Up to date, research on fish spleen is mostly focused on its immune function, and the roles and mechanisms of spleen in the regulation of fish metabolism are still unclear. For this purpose, we established a spleen-deficient model of Nile tilapia (Oreochromis niloticus) by splenectomy and integrated lipidomics and transcriptomics to study the changes and mechanisms of lipid metabolism in splenectomy tilapia so as to understand the effect of spleen on lipid metabolism in tilapia. We found that splenectomy can lead to lipid deposition in the liver of tilapia, significant changes in liver and serum lipid mass spectrometry, abnormal lipid metabolism, decreased anti-oxidative stress ability, and being more prone to lipid toxicity and fatty liver. Combined with the results of transcriptomics, we found that splenectomy resulted in down-regulation of differentially expressed genes in "cellular iron ion homeostasis," "extracellular region," "small molecule binding," and "TGF-beta signaling pathway," and iron metabolism-related genes such as tfa, bmp2b, bmp6, hamp, and slc40a1, etc. were closely related to differential lipid changes. Therefore, it is speculated that the abnormal lipid metabolism in tilapia after splenectomy is closely related to iron metabolism, and its molecular mechanism may be related to the hepcidin regulatory pathway—BMP-SMAD signaling pathway. This study can provide a new understanding of the relationship and mechanism between immune and nutritional metabolism in fish and also provide new ideas for the study of fish hepatic diseases.