In mammals, fatty acid transport protein 1 (FATP1) is involved in cellular long-chain fatty acid (LCFA) uptake and activation, especially in processes of transportation, oxidation and triglyceride synthesis. However, the role of Fatp1 in invertebrates, especially decapod crustaceans, is still poorly understood. In this study, the cDNA of a fatp1 gene of a decapod crustacean, mud crab Scylla paramamosain, was cloned and functionally characterized. The fatp1 gene encoded a polypeptide of 643 amino acids that possessed all the typical features of the Fatp family, and shared high homology with the other Fatp orthologs of crustaceans. The relative expression levels of fatp1 were higher in metabolically active tissues such as hepatopancreas, stomach and gill than the other parts of crabs. Knockdown of the fatp1 gene in vivo reduced triglyceride and total lipid levels in the hepatopancreas, and increased the tissue expression levels of genes related to fatty acid transportation, allocation and hydrolysis including long-chain acyl-CoA synthetase 3/4 (acsl3/4) and carnitine palmitoyl transferase 1 (cpt1), and decreased expression levels of genes related to fatty acid synthesis such as acetyl-CoA carboxylase (acc) and fatty acid synthase (fas). Increased dietary n-3 LC-PUFA levels resulted in the up-regulation of fatp1 gene expression in the hepatopancreas, and the increase in LC-PUFA content, especially EPA and DHA, in both polar and nonpolar lipids in hepatopancreas and muscles of crabs. The data collectively suggested that the fatp1 gene, identified in S. paramamosain, might play important roles in regulating fatty acid absorption, utilization and allocation in crustaceans.