This study was aimed to investigate the protective effect of potent humanin analogue (HNG) supplementation to freezing media on freezing-thawing induced human sperm damage. We collected semen samples with normal sperm parameters from 15 healthy men. After the swim-up processing, the motile spermatozoa from each of the men were allocated to four equal groups: In the control group, the spermatozoa were frozen in media without HNG supplementation. In the other three groups, the spermatozoa were frozen in media supplemented with different concentrations of HNG (2 μM, 10 μM and 20 μM, respectively). We analyzed the sperm motility, viability, sperm mitochondrial membrane potential, apoptosis, sperm DNA fragmentation index (DFI), reactive oxygen species (ROS) and malondialdehyde (MDA) levels, and caspase-3 activity for the sperm in each group. As a result, supplementation of HNG with 2 μM, 10 μM and 20 μM to the freezing media all significantly improved sperm motility and viability (all p < 0.05) when compared with the control group. Similarly, we found that supplementation of HNG reduced the damage to the mitochondrial membrane and DNA integrity, and inhibited the reaction of oxidative stress and the activity of caspase-3 in sperm. Although these protective effects increased with the elevated concentration of HNG in the freezing media, a final HNG concentration of 20 μM failed to exert significant improvements when compared with the concentration of 10 μM (all p > 0.05). In conclusion, our results suggested that HNG supplementation to the freezing media could protect sperm cells from freezing-thawing induced sperm damage.