Scylla paramamosain is one of important aquaculture crabs, which has great economical and nutritional value. As we all know, few full-length crab transcriptomes are available. In this study, a library from 12 different tissues including gill, hepatopancreas, muscle, cerebral ganglion, eyestalk, thoracic ganglia, intestine, heart, testis, ovary, sperm reservoir, and hemocyte was constructed and sequenced using Pacific Biosciences single-molecule real-time (SMRT) long-read sequencing technology. A total of 284803 full-length non-chimeric reads were obtained, from which 79005 high-quality unique transcripts were obtained after error correction and sequence clustering and redundant. Additionally, a total of 52544 transcripts were annotated against protein database (NCBI nonredundant, Swiss-Prot, KOG, and KEGG database). A total of 23644 long non-coding RNAs (lncRNAs) were identified. Our study provides a rich set of full-length cDNA sequences for S.paramamosain, which will greatly facilitate S.paramamosain research.