The overall autophagy disorder may be driven by DNA methylation and transcriptional changes regarding the MAPK pathway-related gene Map3k1. Our results indicate that the epigenetic imbalance may cause the activation of the MAPK signaling pathway, triggering a series of downstream responses, which are of great significance for follicular hypoplasia, hyperautophagy, and the metabolic disorders of PCOS. This evidence concerns the gene MAP3K1 and metabolic disease.