Abstract: Targeted degradation techniques use the naturally existing degradation mechanism(s) in eukaryotic cells to specifically degrade harmful substances to maintain and improve cellular homeostasis. The techniques specifically remove misfolded or aggregated proteins, macromolecular complexes, damaged or aged organelles, and some non-protein substances via the ubiquitin-proteasome system (UPS) and the autophagy-lysosome pathway. Among these techniques, the targeting autophagic degradation techniques have many characteristics such as high target selectivity and wide substrate scope, making them promising techniques for the treatment of neurodegenerative diseases, metabolic diseases, and other diseases. At present, the application potential of these techniques is far from being fully developed, especially in the field of plant science. This review details the mechanisms, characteristics, and advantages of targeted degradation techniques based on the autophagy-lysosomal pathway. Moreover, combined with the recent research work of Professor Li Faqiang group in South China Agricultural University, this review focuses on the research of designing and modifying the autophagy adaptors to transport those factors unfavorable to plant growth and development via selective autophagy to the vacuole for compartmentation, so as to develop new crop varieties that can resist viral infection or toxic abiotic components. This review ends with a discussion of the potential applications and challenges of targeted autophagic degradation techniques in plant science and agricultural production.