Background <p>Cryptorchidism is caused by a combination of environmental and genetic variables. This study aimed to identify cryptorchidism-associated susceptibility genes through bioinformatics approaches and validate their dynamic expression patterns in rat models, with the exploration of upstream transcriptional factor (TF) regulatory networks.</p> Methods <p>Three cryptorchidism-related datasets were obtained from the online GEO database. According to the connectivity degrees in the PPI network, the hub genes were identified. Moreover, a surgical cryptorchidism rat model was successfully established for validating the hub genes’ expression by qRT-PCR, Western blot, and immunohistochemical (IHC) staining. Besides, a TF regulatory network was constructed for revealing its potential mechanism in cryptorchidism.</p> Results <p>Based on the differentially expressed genes (DEGs) in three cryptorchidism-related datasets and the connectivity degrees in the PPI network, MAGEA1 was finally identified as a hub gene in cryptorchidism (all <i>P</i> &lt; 0.05). Further experiments validated the expression of MAGEA1 in the surgical cryptorchidism rat model via qRT-PCR, Western blot, and IHC staining (all <i>P</i> &lt; 0.05). Moreover, we also confirmed the roles of apoptosis in cryptorchidism (<i>P</i> &lt; 0.05). Finally, we also predicted the TF-MAGEA1 network for revealing its potential mechanism in cryptorchidism.</p> Conclusions <p>MAGEA1 was revealed as a novel therapeutic target, and apoptosis was found to play vital roles in cryptorchidism. Mechanistically, the TF CTCFL was predicted to positively regulate MAGEA1 transcriptional activity in cryptorchidism. These findings provided initial mechanistic insights into MAGEA1’s biological function during testicular development and established a novel conceptual framework for understanding cryptorchidism pathogenesis.</p>