Background: As one of the most common congenital defects of the musculoskeletal system, clubfoot affects about one in every 1,000 live births. Studies have shown that mutations in the PITX1-TBX4-HOXC transcription pathway may contribute to familial clubfoot and vertical talus. Despite extensive research, the etiology and pathogenesis of clubfoot is still unclear. Therefore, the aim of this study is to identify genes regulated by Pitx1 that lead to the onset of congenital valgus, using a modular analysis method. Methods: Data collection, weighted gene correlation network analysis, enrichment analysis, and data perspective analysis were performed. Results: Three co-expression modules are enriched in clubfoot. Among them, Mynn, Snca, and Actn2 genes are differently and significantly expressed, and they also play an active supervisory role in the dysfunction module, and are considered to be the driving genes for clubfoot. Connectivity analysis revealed that Ubc and Actn2 regulate multiple functional pathways. The enrichment results indicate that the modular genes are significantly involved in striated muscle tissue development, striated muscle contraction, muscle system process, muscle contraction. Furthermore, they are also involved in ubiquinone and other terpenoid-quinone biosynthesis, transcriptional misregulation in cancer, lysosome and other signaling pathways. Finally, pivot ncRNA (including let-7d-5p and Terc) and pivot TF (including Myod1 and Myog) were identified as meaningful regulatory dysfunction modules. Conclusion: The results of this study identified a differentially regulated protein interaction network involved in clubfoot, and revealed its core dysfunction module and potential regulatory factors.