Glutathione-S-transferases (GSTs) play a protective role during spermatogenesis and GST genes may be involved in impaired spermatogenesis. A case–control study was performed to explore the association of genes GSTM1 and GSTT1, two members of GST gene family, with spermatogenesis impairment. The deletion polymorphism distribution of genes GSTM1 and GSTT1 was investigated in 353 patients with azoospermia or oligospermia and 201 fertile controls in Chinese population using multiplex PCR. As a result, the frequencies of null genotype of genes GSTM1 (67.4% versus 57.7%, p = 0.022, OR = 1.516, 95% CI = 1.001–2.168) and GSTT1 (61.8% versus 46.8%, p = 0.001, OR = 1.838, 95% CI = 1.295–2.610) in patients were significantly higher than those in controls. After stratifying patients, the frequencies of null genotype of gene GSTM1 in oligospermia (68.3% versus 57.7%, p = 0.027, OR = 1.580, 95% CI = 1.051–2.375) and GSTT1 in azoospermia (66.9% versus 46.8%, p < 0.001, OR = 2.299, 95% CI = 1.484–3.562) as well as oligospermia (57.9% versus 46.8%, p = 0.025, OR = 1.567, 95% CI = 1.057–2.322) were still significantly higher compared with controls. The results suggested that null genotypes of GSTM1 and GSTT1 are associated with spermatogenesis impairment and may contribute to susceptibility to spermatogenesis impairment and male infertility in Chinese population.