Objective: To explore the relationship between Hashimoto's autoimmune hypothyroidism (HT) and male fertility, focusing on hormonal and seminal factors. Methods: A systematic literature search was conducted across databases such as PubMed, Web of Science, EMBASE, Scopus, Cochrane, and Google Scholar, covering studies published from January 2000 to March 2024. Studies investigating the impact of HT on semen quality parameters and reproductive hormones were included. Pooled effect estimates were calculated using standard mean difference (SMD) and 95% confidence intervals (CI). Results: A total of 8 studies with 8 965 participants were included. HT significantly affected semen quality and reproductive hormone levels. Specifically, there was a notable decrease in progressive morphology (SMD= -0.78; 95% CI: -1.40 to -0.17; P=0.01) and sperm motility (SMD= -1.151; 95% CI: -1.876 to -0.425; P=0.002). In addition, there were no significant changes in reproductive hormones, although there were elevated levels of luteinizing hormone (SMD=0.437; 95% CI: 0.000 to 0.874; P=0.050) and follicle-stimulating hormone (SMD=0.293; 95% CI: -0.171 to 0.758; P=0.216), with a slight impact on testosterone levels (SMD= -1.143; 95% CI: -2.487 to 0.200; P=0.095). Conclusions: This systematic review and meta-analysis provides robust evidence of the detrimental effects of HT on semen quality and reproductive hormones, underscoring the necessity for thorough evaluation and management of thyroid function in male infertility assessments.