Long non-coding RNAs (IncRNAs) perform distinct functions in various biological processes in mammals, including sex differentiation. However, the roles of IncRNAs in other vertebrates, especially in the Chinese soft-shell turtle (Pelodiscus sinensis), remain to be clarified. In this study, we performed genome-wide analysis of the IncRNA expression profiles in gonad tissues and screened numerous sex-specific IncRNAs in the Chinese soft-shell turtle. Of the 363,310,650 clean reads obtained, 5,994 sequences were typed as IncRNAs, of which 4,463 were novel. A selection of sex-specific IncRNAs (female 932, male 449) from femal ovaries and male testis were shown to act on target genes in cis and in trans, and most were involved in gonad differentiation based on Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Furthermore, interactions among the differentially expressed IncRNA-mRNAs and protein coding genes were identified by construction of correlation networks. Overall, our systematic analysis of IncRNA expression profiles in gonad tissues revealed numerous sex-specific IncRNAs in P. sinensis. Thereby, these findings provide new insights into the function of IncRNAs in sex differentiation and highlight a group of candidate IncRNAs for future studies.