Objective: To analyze the correlation between serum homocysteine (Hcy) and both folic acid (FA) and sperm DNA fragmentation index (DFI), so as to provide the evidence for male fertility assessment. Methods: Males who visited and measured the serum Hcy in the Reproductive Medicine Center of Huzhou Maternal and Child Health Care Hospital from September 2022 to September 2023 were selected as the study subjects. Sperm quality parameters and sperm DFI were analyzed by collecting sperm. Hcy and FA were measured by collecting venous blood. Participants were stratified into a high Hcy group (Hcy≥15.0 μmol/L) and a normal group (Hcy<15.0 μmol/L). The correlations between serum Hcy and FA and sperm DFI were evaluated using linear regression models. Results: A total of 173 participants were enrolled, including 39 in the high Hcy group and 134 in the normal group. The sperm concentration in the high Hcy group was significantly lower than that in the normal group [(91.77±61.11)×106/mL vs. (144.21±106.82)×106/mL, P<0.05]. No statistically significant differences were observed in semen volume, sperm motility, curvilinear velocity, straight-line velocity, average path velocity, or sperm morphology normal rate (all P>0.05). The FA level in the high Hcy group was lower than that in the normal group [(4.44±1.79) nmol/L vs. (7.64±3.68) nmol/L, P<0.05]. The sperm DFI in the high Hcy group was higher than that in the normal group [(19.21±8.85)% vs. (13.07±6.43)%, P<0.05]. Serum Hcy level showed a negative correlation with FA level (r=-0.369, P<0.05) and a positive correlation with sperm DFI (r=0.351, P<0.05). Conclusion Serum Hcy level is associated with sperm concentration, FA and sperm DFI, suggesting that serum Hcy may affect sperm quality.