Investigation of sex determination system in Eriocheir sinensis is important because of sex-dimorphism in its growth traits. However, little information about the sex-related genes in embryonic development stages were exposed. To obtain more information of sex determination in Chinese mitten crab, we performed the transcriptome analysis in embryonic development stage (fertilized egg stage, cleavage stage, blastula stage, gastrula stage and heartbeat stage) of Chinese mitten crab using nextgeneration sequencing technology. Thirty-one of 32,088 annotated unigenes were identified as sex-related genes including 16 genes involved in primary sex determination in model organisms and 8 genes of SOX family and 7 genes of DMRT gene family. Heatmap based on the RPKM value in five embryonic development stages indicated that these genes were clustered into two branches. Analysis of the differentially expressed 12 genes, including 3 genes of SOX family, 3 genes of DMRT gene family and 6 genes involved in primary sex determination in model organisms, showed significantly difference between the first three periods (fertilized egg stage-cleavage stage-blastula stage) and the last two periods (gastrula stage-heartbeat stage) and all 12 genes were up-regulated after blastula stage. In conclusion, we inferred that sex determination might be initiated after blastula stage in E. sinensis. Transcriptome analysis from embryonic development stage could provide a background information for further investigation in sex determination of Eriocheir sinensis.