Significance In addition to mediating protein traffic from the endoplasmic reticulum to the Golgi apparatus, coat protein complex II (COPII) vesicles also act constructively as a membrane source for autophagosome biogenesis during autophagy to maintain cellular homeostasis in eukaryotes. Nonetheless, the participation and underlying mechanism of the COPII machinery in the autophagic pathway and autophagosome biogenesis remain elusive in plants. Here, we identified and characterized a distinct population of COPII vesicles consisting of a unique AtSar1d-AtRabD2a nexus, which is required for autophagosome biogenesis through mechanistic connection with autophagy-related (ATG) machinery in Arabidopsis . Our results broadened the understandings of the mechanism underlying COPII function in eukaryotic autophagy and manifested the functional diversity of specific COPII paralogs in plant autophagy and autophagosome biogenesis.