It is of great significance for bivalve aquaculture to promote the growth through nutritional strategy. Phosphatidic acid (PA) is a potential growth-promoting nutraceutical that targets for mammalian target of rapamycin (mTOR) in vertebrates, but its role in invertebrates remains largely unknown. Here, the effects of PA on mTOR and metabolic pathways in bivalve mollusk Sinonovacula constricta were determined by intramuscular injection with di-18 : 2 PA and di-16 : 0 PA. PA (both di-18 : 2 and di-16 : 0 PA) was found to increase the glycogen concentration in the muscle of S. constricta. Di-16 : 0 PA decreased the triglyceride concentration from 0.143 ± 0.04 mmol/g protein to 0.040 ± 0.018 mmol/g protein. The concentration of Asp, Glu, Ala, Cys, Val, Met, Ile, Leu, Phe, Arg, and Pro was reduced by di-18 : 2 PA or/and di-16 : 0 PA. PA increased the mRNA level of mTOR and the phosphorylation levels of eIF4E binding protein 1 and p70S6 kinase 1. Furthermore, PA decreased the protein level of microtubule-associated protein 1 light chain 3 Ⅱ/Ⅰ and the mRNA level of AMP-activated protein kinase. The mRNA expressions of two key enzymes of glycolysis (pyruvate kinase and glucokinase) were also upregulated by both PA, while the mRNA level of glucose transporter 1 was increased by di-18 : 2 PA. Di-16 : 0 PA decreased the mRNA level of phosphoenolpyruvate carboxykinase. The mRNA levels of sterol responsive element binding protein, fatty acid synthase, and acetyl-CoA carboxylase were increased by both PA. The mRNA level of stearoyl-CoA desaturase was increased by di-18 : 2 PA. Both PA species increased the mRNA levels of key enzymes involved in tricarboxylic acid cycle (citrate synthase and NADP-isocltrate debydrogenase). Our results indicated that PA activated mTOR signaling pathway, subsequently leading to the increase of anabolism and the inhibition of catabolism in S. constricta.