Despite the growing evidence that the presence of cryptorchidism increases the risk of azoospermia, the common mechanisms via which it occurs remain incompletely elucidated. This research was conducted to gain a deeper understanding of the molecular mechanisms that contribute to the onset and progression of this complication. In total, 197 common DEGs (182 down-regulated and 15 upregulated genes) were chosen for further investigation. The significance of cell cycle and metabolic regulation in the onset and progression of both diseases was highlighted by functional analysis. Eventually, nine important hub genes were identified using cystoHubba, including CCNB1, PCNA, AURKA, CCT5, CCT2, STIP1, UBE2N, RUVBL1, and HSF1. Our research elucidates a common pathogenesis between cryptorchidism and azoospermia. These common pathways and hub genes might inspire new avenues of investigation into underlying mechanisms.