Invertebrates change the metabolite concentrations in their bodies to adapt to environmental salinity. The kuruma shrimp Marsupenaeus japonicus is one such invertebrate. It lives in coastal areas and is also known to change free amino acid concentrations depending on environmental salinity. To examine the relationship between the concentrations of metabolites, including amino acids, in the kuruma shrimp with environmental salinity, metabolome analysis was performed on the abdominal muscle of shrimps acclimated at 17, 34 and 40‰ salinity for 24 h. Principal component analysis revealed that the accumulation patterns of metabolites using the 111 metabolites detected in the shrimps exposed to different salinities were depicted in a salinity-dependent manner. The concentrations of alanine and glutamine were increased following exposure to increasing levels of salinity, suggesting that these free amino acids function in intracellular osmoregulation of the kuruma shrimp. Furthermore, the concentration of glycolytic metabolites was significantly decreased at high salinity. The concentrations of most of the metabolites related to the tricarboxylic acid (TCA) cycle also tended to decrease at high salinity. Considering the levels of expression of the genes related to various metabolic pathways, it seems that glycolysis is accelerated at high salinity.