The swimming crab Portunus trituberculatus is an important farmed species in China. Ammonia-N represents a major physiological challenge for crab culture and the hepatopancreas plays a major role in physiological adaptation processes. To better understand the molecular mechanism of the crab in response to ammonia-N stress, we performed a transcriptome analysis in the hepatopancreas of P. trituberculatus challenged with ammonia-N stress (5 mg/L), using the high-throughput sequencing technology. In total, 52,280 unigenes were obtained from the hepatopancreas of P. trituberculatus, with an average length of 678 bp. Functional categorization and pathways showed some differentially expressed genes were involved in amino acid and nucleobase metabolism, energy metabolism, antioxidation, immune response, reproduction, moulting and material transport. The differential expression patterns of eight randomly selected annotated genes were validated by quantitative real-time PCR (qPCR). Results revealed a substantial number of genes modified by ammonia-N stress and a few significant ammonia acclimation pathways, which will serve as an invaluable resource for revealing the molecular basis of physiological adaptation mechanism in P. trituberculatus.