This is the first comprehensive transcriptome dataset report for the AG of proliferation phase and secretion phase in E. sinensis. A total of 72,000 unigenes and 4,027 DEGs were obtained. Comparative transcriptomic analysis showed that IAG, SXL, TRA-2, SRY, FTZ-F1, FOXL2, and cytochrome p450 might play important roles in maintaining the male physiology and morphology. Ubiquitin, serpin, cathepsin A, and cathepsin D genes may have a direct influence on spermatogenesis. Ribosomes are the most prominent pathway and their related genes might be the key elements in relation to cell growth and secretion. In insulin-like receptor signaling pathway, Unigene10231 may indirectly regulate spermatogenesis and male secondary sexual characteristic development, and whether CL1931 participates in sexual differentiation still needs further study. In neuroactive ligand-receptor interaction pathway, octopamine receptor was significantly upregulated and 5-HT receptor 1 and melatonin receptor were significantly downregulated. This revealed the key regulation mechanism in male mating and aggressive behavior. Our comparative transcriptomic analysis provides new insights into the genome-wide molecular mechanisms of AG development and the regulatory mechanisms of male important traits of E. sinensis.