Congenital domestic absence of vas deferens (CBAVD) is a common factor in male infertility, and percutaneous epididymal sperm aspiration (PESA) combined with intracytoplasmic sperm injection (ICSI) is a primary clinical treatment, but the effect of the sperm obtained on pregnancy outcome remains to be explored. This study aimed to investigate the relationship between sperm motility with clinical outcome of PESA–ICSI in infertile males with CBAVD. A cohort of 110 couples was enrolled. In total, 76 infertile males were included in the high motility group, while the remaining 34 males were placed in the low motility group. Clinical pregnancy, embryo implantation rate and live birth rate were included as the primary outcome. After all follow-ups, we found that the high motility group achieved higher normal fertilization rates, cleavage rates, transplantable embryo rates and high-quality embryo rates than those in low motility group (normal fertilization rate, 78.2 ± 11.7% vs. 70.5 ± 10.2%, P = 0.003; cleavage rate, 97.1 ± 2.9% vs. 92.3 ± 3.0%, P = 0.000; transplantable embryo rate, 66.8 ± 14.9% vs. 58.6 ± 12.6%, P = 0.009 and high-quality embryo rate, 49.9 ± 10.5% vs. 40.5 ± 11.2%, P = 0.000). Additionally, compared with the low motility group, the clinical pregnancy rates, embryo implantation rates, and live birth rates in the high motility group were significantly increased (pregnancy rate, 61.8% vs. 26.5%, P = 0.009; embryo implantation rate, 36.5% vs. 18.0%, P = 0.044; live birth rate, 55.3% vs. 17.6%, P = 0.000). We concluded that the motility of sperm obtained by PESA affected the clinical outcome of ICSI in infertile males with CBAVD.