This study was conducted to investigate the regulation mechanism of dietary lysine (Lys) content in Litopenaeus vannamei after partially replacing fish meal with fermented soybean meal, where 0%, 0.25%, 0.50%, 0.75% and 1.00% of crystalline lysine was added to the basic feed (recorded as Lys0, Lys25, Lys50, Lys75 and Lys100). Litopenaeus vannamei with an initial body weight of (2.0±0.1) g were selected for a 56-day feeding trial in an indoor cement pond fed with above 5 isonitrogenous and iso-lipidic experimental diets respectively, and those in Lys0 and Lys75 groups under went metabolomics and transcriptomic analysis based on significantly different growth performance, crude protein and lipid content in muscle, hepatopancreas health as well(P<0.05). The results showed that compared to Lys0 group, a total of 28 different metabolites were detected in Lys75 group, among which 2 metabolites were down-regulated and 26 metabolites were up-regulated; Signal pathway analysis was performed on 7 different metabolites annotated to the KEGG database, and 4 important metabolic pathways were screened out, namely glycine, serine and threonine metabolism, arachidonic acid metabolism, Sphingolipid metabolism, glycerophospholipid metabolism. In the Lys75 group, choline was significantly down-regulated in the hepatopancreas(P<0.05), the expression of γ-butyl betaine plus dioxygenase genes was significantly up-regulated(P<0.05), and the expressions of hexokinase genes and acetylcholinesterase genes were significantly down-regulated(P<0.05). The results indicated the increase of dietary lysine level due to crystal lysine addition helped the β-oxidation of fatty acids in the hepatopancreas, playing a role in protein saving and protecting the health of the hepatopancreas as well, thus promoted the growth of the shrimp.