Abstract To ascertain whether COVID-19 infection affects sperm quality and measure the scale of the effects. A cross sectional study and a longitudinal study were conducted during the SARS-CoV-2 pandemic (from September 7th 2022 to late January 2023) in China. 604 patients participated in the cross sectional study; 140 in the longitudinal study with 149 unaffected natural controls. The cross sectional study included participants who produce semen sample after COVID-19. The longitudinal study included COVID-19 positive participants who could provide semen samples before and after the infection. In addition, patients unaffected by the infection who could provide two consecutive semen samples over the same period were included as controls for the longitudinal study. Conventional sperm quality parameters including sperm count, motility, morphology and more recent parameters such as sperm DNA fragmentation index (DFI) and sperm chromatin immaturity were observed. In the cross sectional study, the exposure group demonstrated significantly lower total sperm count (159.58 × 106 vs. 185.42 × 106, P = 0.042), lower percentage of grade A sperms (5.37% vs. 8.45%, P = 0.009), lower progressive motility (24.74 ± 14.96% vs. 28.73 ± 16.65%, P = 0.023), lower total motility (32.04 ± 18.03% vs. 36.91 ± 20.86%, P = 0.022), and higher sperm DFI (17.50% vs. 11.75%, P = 0.030) than the controls. In the longitudinal study, after the infection, patients showed lower total sperm count (131.80 × 106 vs. 173.63 × 106, Δd = -20.49 × 106, P = 0.018 ), lower percentage of grade A sperms ( 2.61% vs. 8.50%, Δd = -3.18%, P