Glyphosate-based herbicide (GBH) is a popular herbicide, which may contaminate the water environment and affect aquatic animals. In this study, testes morphology, physiology function, apoptosis pathway, and spermatozoa quality of Chinese mitten crab (Eriocheir sinensis) were evaluated after 7 days of GBH exposure (48.945 mg/l,1/2 of the 96 h LC50 value of GBH). Results showed that GBH induced spermatogenesis disorder by H.E. staining. The obvious vacuolar degenerations and fewer spermatids of the testes accompanied by decreased primary spermatocytes-type seminiferous tubules (PSc-STs) were observed. The extensive apoptosis of spermatids by TUNEL staining was visible. Meanwhile, testes’' characteristic enzyme activities associated with spermatogenesis, including lactate dehydrogenase (LDH) and acid phosphatase (ACP) were significantly decreased. Testes suffered oxidative damage as reflected by the significant decrease in superoxide dismutase (SOD) activities, the significant increase in malondialdehyde (MDA) contents, and heat shock proteins (HSP-70) mRNA expression. Further studies demonstrated that GBH induced apoptosis of testes through the mitochondrial apoptotic pathway by upregulating the relative mRNA expression of cysteinyl aspartate specific proteinase 3 (Caspase-3), Bcl-2-associated X protein (Bax), and downregulating B-cell lymphoma 2 (Bcl-2). Oxidative damage may be one of the causes of GBH-induced apoptosis in testes. After GBH exposure, the morphology of spermatophores was changed. The survival and the acrosome reaction (AR) ratio of spermatozoa was significantly decreased. Altogether, these results demonstrated that GBH affects spermatogenesis, spermatophore and spermatozoa quality of E.sinensis, which provides novel knowledge about the toxic effects of GBH on the reproductive system of crustaceans.