The present study investigates the effects of dietary phosphatidylcholine (PC) deficiency and its addition on growth and physiological and biochemical indicators of juvenile Eriocheir sinensis under different oil sources. There were no significant differences in the growth and feed utilization between the vegetable oils and fish oil (FO) groups under PC-devoid conditions. In contrast, the FO and perilla oil (PO) groups showed better growth-promoting effects and higher feed utilization than the safflower oil (SO) and olive oil (OO) groups under 3% PC-added condition. Both dietary PC and oil sources (FO or PO) could inhibit lipid accumulation of the whole crab, and dietary PC also observably facilitated whole-body protein deposition. In addition, dietary FO and PO increased the burden of the antioxidant system and the risk of lipid peroxidation in juvenile E. sinensis. Meanwhile, diets supplemented with PC effectively alleviated oxidative stress and lipid peroxidation caused by dietary FO and PO. The composition of fatty acids in muscle and hepatopancreas was positively associated with that in diets. Compared with SO and OO, FO and PO significantly reduced the lipid deposition in the hepatopancreas at 3% PC supplementation, possibly because FO and PO formed new physiological-active PC contained n-3 polyunsaturated fatty acids (PUFAs) with dietary PC through activating PC remodeling reaction, and promoting fatty acid utilization, and finally inhibiting the lipid accumulation in the hepatopancreas. This study indicates that FO and PO are better lipid sources (LSs) for E. sinensis, providing alternative oil sources in the crab diet in combination with PC supplementation.