The half-smooth tongue sole (Cynoglossus semilaevis), one of the most economically-important fish species in China, exhibits sexually dimorphic growth. An understanding of sex-related gene expression patterns in the tongue sole may inform sex regulation and breeding processes that increase fish production. However, the gene expression patterns during gonad development in the tongue sole remain unknown. In this study, transcriptome sequencing analyses were performed during gonad differentiation in the tongue sole, namely, at 62 days post-hatching (dph), 100 dph, 120 dph, and 150 dph. Differentially expressed genes associated with sex differentiation and gonad development were identified at each time point. Trend analysis showed that gene expression patterns varied over time. These expression patterns either explained common, non-sexually-dimorphic features or indicated significant sexual dimorphism. Transcript structure analyses identified both sex and time differences among samples. This study investigated the time-dependent expression patterns of several sex-related genes, including Dmrt1, Amh, Foxl2, aromatase encoding gene, Esr, and the Sox gene family, during gonad differentiation in the tongue sole. These results might clarify the significant sexual differences during early development in the tongue sole and might provide insight into the mechanisms controlling sex differentiation and development.