Procambarus clarkii is one of the freshwater lobsters which has important economic value in China. However, long-term high-density farming and inbreeding have brought many negative effects on the cultivation of P. clarkii, such as slow growth, small size, frequent diseases, and the difficulty of artificial breeding caused by the asynchrony of gonadal development, which have severely restricted the further development of P. clarkii aquaculture. In order to find candidate genes involved in ovary development, immunity and muscle growth of P. clarkii for improving the production performance of this species, the transcriptomes of ovary, hepatopancreas and muscle of P. clarkii were sequenced by a new generation of high throughput sequencing technology. After quality control and assembly, the sequences acquired were blasted against NR, Swiss-Prot, pfam, COG, GO and KEGG databases, and then cluster analyses were performed. In total, 53 006 final unigenes with an average length of 1 194 bp were obtained. Pairwise comparison of sequencing libraries of 3 tissue samples revealed that 20 382 differentially expressed genes (DEGs) were found in ovary vs. hepatopancreas group, 12 753 DEGs were found in hepatopancreas vs. muscle group, 21 629 DEGs were found in muscle vs. ovary group. Gene ontology analysis indicated that some DEGs were annotated into "reproduction", "reproduction process", "immune system process" and "growth" GO terms. KEGG pathway analysis showed that some DEGs were enriched in signaling pathways related to ovarian development, immunity and muscle growth. Based on GO functional classification and KEGG pathway analysis, a large number of candidate genes related to ovarian development, immunity and muscle growth of P. clarkii were screened, such as vitellogenin, vitellogenin receptor, Toll-like receptor 2, Toll-interacting protein, myostatin, 5-hydroxytryptamine receptor, etc. The results of this study enriched the gene resources of P. clarkii and could provide basic data for the further genetic breeding and immunity research of this commercial species.