Objective To determine the association of single nucleotide polymorphism (SNP) locus C321A in human protamine 1 (PRM1) with male infertility in Chinese Han population. Methods A total of 174 infertile men were recruited as the observation group and 172 fertile men were recruited as the control group. Routine semen analysis was performed. Restricted enzyme digestion and DNA direct sequencing of C321A in PRM1 gene of the infertile and fertile men were conducted to identify the genotype of C321A SNP locus. Results The frequency of AA genotype of PRM1 C321A was significantly different between the infertile men (8.05%) and the fertile men (2.33%, P < 0.01) and it was associated with increased risk of male infertility (■ = 4.24; 95% CI: 1.33, 13.51). Moreover, it was discovered that sperm progressive motility as well as normal morphology rate of AA genotype were dramatically decreased compared with that of CC genotype (P < 0.05), which would probably lead to infertility. Conclusions PRM1 C321A polymorphism is associated with male infertility as well as routine semen characteristics in Chinese Han population.