The endocrine-disrupting effects of glyphosate, particularly its impact on human sex hormones, remain poorly understood. This study aimed to investigate the association between glyphosate exposure and reproductive toxicity, focusing on cholesterol homeostasis and hormone synthesis pathways. Using data from the 2013-2016 National Health and Nutrition Examination Survey (NHANES), we found that glyphosate exposure was significantly associated with a reduction in Free Androgen Index (FAI) (β = -3.27; 95 % CI: -4.45 to -2.10; p < 0.001). Mediation analysis showed that serum cholesterol and albumin explained 15.8 % and 12.1 % of this association, respectively. Network toxicology analysis indicated that aminomethylphosphonic acid (AMPA), the main metabolite of glyphosate, may interfere with steroid hormone biosynthesis and bile acid metabolism. Molecular docking revealed strong binding affinities between AMPA and key cholesterol metabolic and testosterone synthesis enzymes, including CYP7A1, CYP11A1, and CYP17A1. Finally, we validated these findings in a mouse model, where exposure to glyphosate-based herbicides led to decreased serum cholesterol and testosterone levels, increased hepatic CYP7A1 expression, and reduced testicular CYP11A1 and CYP17A1 expression. These results highlight the critical role of disrupted cholesterol homeostasis in the liver-testis axis in glyphosate-induced reproductive toxicity, emphasizing the urgent need to re-evaluate safety standards and regulatory policies.