Mammalian endoplasmic reticulum (ER) exit sites export a variety of cargo molecules including oversized cargoes such as collagens. However, the mechanisms of their assembly and organization are not fully understood. TAN GO1L is characterized as a collagen receptor, but the function of TAN GO1S remains to be investigated. Here, we show that direct interaction between both isoforms of TAN GO1 and Sec16 is not only important for their correct localization but also critical for the organization of ER exit sites. The depletion of TAN GO1 disassembles COPII components as well as membrane-bound ER-resident complexes, resulting in fewer functional ER exit sites and delayed secretion. The ectopically expressed TAN GO1 C-terminal domain responsible for Sec16 binding in mitochondria is capable of recruiting Sec16 and other COPII components. Moreover, TAN GO1 recruits membrane-bound macromolecular complexes consisting of cTAGE5 and Sec12 to the ER exit sites. These data suggest that mammalian ER exit sites are organized by TAN GO1 acting as a scaffold, in cooperation with Sec16 for efficient secretion.