Breast cancer is a heterogeneous disease and a prevalent form of aggressive tumors in females. It remains a leading cause of mortality among adult and older women worldwide, with therapeutic resistance leading to a barrier for reliable clinical outcomes. Many studies are exploring the relationship between epigenetic dysregulation and autophagy, driving therapy resistance, tumor progression, and metabolic changes. Sudden modifications in histone tails, non-coding RNAs, and DNA methylation patterns directly modify autophagic genes, while dysregulated autophagy conversely alters the epigenetic landscape under therapeutic stress. Recent studies have shown that molecular mechanisms link epigenetic alterations with autophagy regulation in breast cancer. This literature review systematically selected studies highlighting the molecular mechanism of autophagy dysregulation and its role in chemotherapy, endocrine, and targeted therapy resistance in breast cancer. This article briefly discusses the clinical implications of epigenetic biomarkers for early detection and treatment response prediction. Furthermore, we discussed new therapeutic methods combining autophagy inhibitors and epigenetic modulators, emphasizing the role of advanced medicine approaches powered by AI-driven drug discovery. The main idea of this literature review is to provide an in-depth insight into the epigenetic autophagy link in breast cancer and shed light on promising therapeutic outcomes overcoming chemotherapeutic resistance.