Glyphosate (GLY) exposure, both exogenous and endogenous, is a global concern. Multiple studies of model systems in vitro and in vivo have demonstrated the potential toxic effects of GLY exposure on human organs, particularly the liver and renal system. However, there is currently limited epidemiological evidence establishing a link between GLY exposure and hepatorenal function in the general population. In this study, a multivariable linear regression model and forest plots were employed to evaluate the connection between urinary GLY and biomarkers of hepatorenal function in 2241 participants from the National Health and Nutrition Examination Survey 2013-2016. Additionally, subgroup analyses were conducted based on age, gender, race, BMI, and chronic kidney disease (CKD). Alkaline phosphatase (ALP), alanine aminotransferase (ALT), aspartate aminotransferase (AST), AST/ALT and fibrosis 4 score (FIB-4) all increased with elevated urinary GLY concentrations after adjusting for potential confounders, while albumin (ALB) exhibited the opposite trend, particularly among younger, female, non-Hispanic white, overweight, and CKD participants. Furthermore, individuals in the third tertile had a greater risk of liver dysfunction than those in the first tertile after categorizing urinary GLY concentrations. However, our study showed no proof that GLY exposure affects the ratio of urine albumin to creatinine (ACR) or serum creatinine levels. Overall, these results imply that GLY exposure may have adverse effects on human liver function.