Precocity is a common problem in aquaculture of Chinese mitten crab (Eriocheir sinensis). To discover and clone important functional genes, the transcriptome of Y-organs of precocious and normal female crabs were sequenced by Illumina Hiseq 2000 high-throughput sequencing technology, and comparative transcriptome study was conducted. The results showed that precocious and normal crabs had 44 619 538 and 43 052 958 clean reads, respectively. Comparison between the sequencing data from precocious and normal female crabs revealed 2 655 differentially expressed genes. The differentially expressed genes GO functions in the transcriptome library were broadly divided into three major ontology (biological processes, cellular component and molecular function categories) of 42 branches. Data in the transcriptome from 134 differentially expressed genes could be divided into 4 classes taking the KEGG database as a reference, according to the metabolic pathway, including synthesis and degradation of ketone bodies, butanoate metabolism, neurotrophin signaling pathway, and base excision repair. By RNA-seq, we obtained abundant transcriptome information that could contribute to novel gene identification, causes and prevention of precocity, and research of Y-organs in Eriocheir sinensis.