Background: Male infertility remains a significant clinical challenge. The KISS1R-CATSPER3 signaling axis and acrosomal integrity are vital for fertilization, yet their regional expression patterns in subfertile men are not fully characterized. Objectives: This study investigated regional expression patterns of KISS1R and CATSPER3 and evaluated acrosomal integrity in oligozoospermic and normozoospermic individuals, accounting for demographic confounders. Methods: A total of 52 participants were selected from 568 candidates and divided into normozoospermic (n = 26) and oligozoospermic (n = 26) groups. Analysis included qPCR and immunofluorescence for KISS1R and CATSPER3. Regional expression was independently scored by blinded researchers. Statistical models were adjusted for age and body mass index (BMI). Results: Acrosomal integrity was significantly lower in the oligozoospermic group (p < 0.001). After adjusting for age and BMI, overall protein expression of CATSPER3 and KISS1R remained significantly lower in oligozoospermic men (p < 0.05). Regional analysis showed that CATSPER3 head staining differences disappeared after adjustment, whereas lower tail expression persisted. Higher KISS1R head expression in oligozoospermic men remained significant. qPCR showed no differences in KISS1R or CATSPER3 mRNA levels (p > 0.05), indicating post-translational regulation. Conclusions: KISS1R-CATSPER3 axis downregulation is a hallmark of oligozoospermia that persists independently of age and BMI. Regional protein instability, despite stable mRNA levels, suggests that post-translational regulation is critical for fertility. These markers may serve as potential diagnostic or therapeutic indicators for male infertility.