Hypoxia-inducible factor-1 alpha (HIF-1 alpha) participates in the regulation of spermatogenic function in rats with varicocele (VC), and the PI3K/Akt pathway plays an important role in it. In the present research, we applied the CRISPR/Cas9 gene editing technique to silence the HIF-1 alpha gene of VC rat testis, to explore the effect of HIF-1 alpha on apoptosis of spermatogenic cells in VC rats through the PI3K/Akt pathway. Sprague Dawley rats were randomly assigned to four groups, including the normal rat group (group N), VC model group (group V), VC + HIF-1 alpha-lentivirus group (group H), and VC + luciferase-lentivirus group (group L). Apoptosis of spermatogenic cells in rat testis was tested by TUNEL Kit. The morphologic changes of seminiferous tubules were viewed by a light microscope. Expressions of VEGF, Akt, p-Akt, p70S6K, and p-p70S6K were detected by means of Western blot, immunofluorescence, or immunohistochemistry methods. One-way ANOVA was applied to analyze the diverseness between groups. Compared with group N, the distribution of germ cells was disordered, apoptosis of spermatogenic cells increased significantly, and the expression of VEGF, p-Akt, and p-p70S6K was also increased in group V. Compared with group V, the damage of seminiferous epithelium in group H was improved, and the arrangement of the seminiferous epithelium was almost orderly. Apoptosis of spermatogenic cells decreased significantly, and the expression of VEGF, p-Akt, and p-p70S6K protein was decreased (P < 0.05). There was no significant difference between group N and group H (P > 0.05). In conclusion, HIF-1 alpha is regulated by hypoxia in rats with varicocele to regulate its downstream gene VEGF which regulates spermatogenesis, and the PI3K/Akt signaling pathway plays a regulatory role in this process.