Sexual dimorphism is widespread in animal kingdom and has been a hot topic in biology for a long time. In particular, the sex of the Mauremys mutica is determined by incubation temperature, however, the molecular mechanism of temperature response is still unclear. In order to understand the molecular mechanism of the sex differentiation of turtles, this study made a preliminary comparative analysis of the sex-differentiated lncRNAs and their target genes in the transcripts of M. mutica. First, the Illumina deep sequencing platform was used to perform comparative transcriptomics analysis of the testis and ovary of M. mutica by RNA-Seqs and screened to identify male and female differential transcripts. A total of 8 237 differentially expressed mRNAs and 9 573 differentially expressed lncRNAs were screened. Through GO functional annotation and KEGG pathway enrichment analysis, we found that these differential transcripts were mainly involved in the sex differentiation and gonadal development of turtles. In addition, a series of target genes related to reproductive development (gonad development and sex differentiation) regulated by DE lncRNA were obtained through the analysis of cis- and trans- effects. This study provides clues for further elucidating the temperature-dependent sex differentiation mechanism of M. mutica, and especially, it lays the foundation for further exploring the use of the sex determinants of turtles to conduct research on animal sexuality control breeding techniques for turtles.