Lipid accumulation in ovaries is essential for reproductive success in decapods. Understanding of the mechanism of ovarian lipid accumulation is still in its infancy. In this study, we investigated lipid compositions of ovaries and hepatopancreas throughout vitellogenesis and hemolymph in the late-vitellogenic stage in the mud crab Scylla paramamosain. Total lipid content in ovaries consecutively increased from the early to late stage, and the main accumulated lipids were phosphatidylcholine (PC), alkenylglycerophosphoethanolamine (alkenyl-PE), triacylglycerol (TG), cholesteryl ester, and cholesterol. The lipid composition of hemolymph indicated that PC, alkenyl-PE, diacylglycerol (DG), ether DG, monoacylglycerol, and cholesterol were the main lipids transferred to ovaries from hepatopancreas. In hepatopancreas, the total lipid content appeared to increase during vitellogenesis and the late stage was significantly different from early and mid-stages. TG was the predominant lipid class that slightly decreased from the early to mid-stage, but dramatically increased in the late stage. In contrast, PC and alkenyl-PE significantly increased from the early to mid-stage and remained constantly in relatively low proportion until the late stage. These findings suggested PC and alkenyl-PE in the hepatopancreas likely play critical roles in regulating lipid transfer. Esterified fatty acids in ovaries and hepatopancreas were mainly C16:0, C18:0, 16:1, C18:1, C18:2, C20:4, C20:5, and C22:6, of which highly unsaturated fatty acids (HUFA) primarily occurred in alkenyl-PE and phosphatidylserine (PS) but not PC. In hemolymph, PC was abundant in HUFA besides of saturated fatty acids (SFA) and monounsaturated fatty acids (MUFA), while PS was predominantly composed of SFA and MUFA, implying a transformation of HUFA between phospholipids prior to transfer. These findings highlight the importance of phospholipid metabolism in the hepatopancreas to ovarian lipid accumulation. Our study provides novel insights into the mechanism of ovarian lipid accumulation in decapods.