The invention discloses a vertical tray fermentation system. The vertical tray fermentation system comprises a vertical fermentation tray, a tray loading machine, a tray sliding device and a tray rail replacing device; the vertical fermentation tray is born and slid on the tray sliding device and a tray rail replacing device, the tray loading machine is arranged above the vertical fermentation tray and the end part of the tray sliding device; the tray rail replacing device is arranged and mounted at the end part of the tray sliding device; a fermentation method of the vertical tray fermentation system comprises the following steps: S1, preparing the system, S2, mixing materials, S3, stirring the materials, S4, crushing the materials, S5, loading the materials into the tray, S6, sliding the tray and fermenting the materials, S7, discharging the materials from the tray, S8, replacing rails for the tray and making the tray circularly charge the materials. The technical problems to be solved by the vertical tray fermentation system are to lower manufacturing and processing difficulties and manufacturing and using costs of the vertical tray fermentation system, avoid operation processes of stacking, unstacking, tray dumping, material pouring and the like, and facilitate long-distance transportation.