Ovarian development is a complex and dynamical process regulated by the coordinated actions of the hepatopancreas and ovary. In mammals, lipids provide necessary energy for oocytes to mature, whereas their regulatory role in crustaceans is not fully understood. This study compares lipid mobilization and deposition in hepatopancreas and ovary of the swimming crab at different stages of ovarian maturation. The results revealed that cholesterol (CHO) and triglyceride (TG) content in hepatopancreas increased with ovary development increased from stage I to Ⅲ, and then decreased at stage V, while those content in ovary significantly increased from stage I to V. Additionally, apolipoprotein (ApoA and ApoB) contents in hepatopancreas and ovary increased significantly during ovary development. Moreover, the highest expression levels of cholesterol transport related genes (srb, ldlr, lrp2 and abcg1) were observed in the hepatopancreas at stage Ⅲ and in the ovary at stage Ⅳ. Furthermore, as ovary development form stage I to Ⅳ, the hepatopancreas up-regulated the expression levels of genes related to lipid anabolism (fas, acc, g6pd, and 6pgd) and fatty acid transport (fabp9 and fatp4). Concurrently, genes related to lipid catabolism (il) and fatty acid β-oxidation (acox2 and acox3) in the hepatopancreas were down-regulated. Differently, with the ovary development increased from stage I to Ⅳ, the ovary up-regulated gene expression levels involved in lipid anabolism (acc, 6pgd, g6pd, dgat1, and gpat3), fatty acid synthesis (elovl and elovl4) and fatty acid β-oxidation (cpt1, cpt2, acox1, and acox3). The mRNA expression levels of lipolysis (tgl) and fatty acid transport (fabp1, fbap9, and fatp4) in ovary were down-regulated. Overall, these findings demonstrate that the hepatopancreas and ovary exhibit different responses to lipid metabolism during ovarian development.