Autophagy is a degradative pathway essential for recycling cytoplasm, generating energy, and maintaining cellular homeostasis in all eukaryotic cells. The most prevalent form, macroautophagy, involves the formation of a double-membrane vesicle called the phagophore, which matures into an autophagosome. The cargo is then degraded and the macromolecules are released back into the cytosol. Over the past two decades, significant progress has been made in understanding the molecular mechanisms of autophagy through studies in yeast and other eukaryotes. However, many aspects remain unclear, including the phagophore formation process, regulatory mechanisms, and the functions of most autophagy-related proteins. This review focuses on macroautophagy, discussing its discovery, the donor membrane that forms the phagophore, and the core molecular machinery involved in autophagosome formation. Key components such as the Atg1 kinase complex, Atg9, PtdIns3K complexes, and Ubl conjugation systems are described, along with their roles in autophagy. Structural studies of these proteins have provided insights into their interactions and functions, but many proteins still lack detailed structural information. Future research directions include elucidating the detailed mechanisms of autophagosome biogenesis and advancing structural studies to better understand the regulation and function of autophagy-related proteins.Autophagy is a degradative pathway essential for recycling cytoplasm, generating energy, and maintaining cellular homeostasis in all eukaryotic cells. The most prevalent form, macroautophagy, involves the formation of a double-membrane vesicle called the phagophore, which matures into an autophagosome. The cargo is then degraded and the macromolecules are released back into the cytosol. Over the past two decades, significant progress has been made in understanding the molecular mechanisms of autophagy through studies in yeast and other eukaryotes. However, many aspects remain unclear, including the phagophore formation process, regulatory mechanisms, and the functions of most autophagy-related proteins. This review focuses on macroautophagy, discussing its discovery, the donor membrane that forms the phagophore, and the core molecular machinery involved in autophagosome formation. Key components such as the Atg1 kinase complex, Atg9, PtdIns3K complexes, and Ubl conjugation systems are described, along with their roles in autophagy. Structural studies of these proteins have provided insights into their interactions and functions, but many proteins still lack detailed structural information. Future research directions include elucidating the detailed mechanisms of autophagosome biogenesis and advancing structural studies to better understand the regulation and function of autophagy-related proteins.