The invention discloses an automatic control storage system of a microwave vacuum drier. The automatic control storage system comprises a controller, a microwave drying tank body and supporting frames which are used for supporting the microwave drying tank body. Compared with the prior art, the automatic control storage system is further provided with a track and a storage chamber, wherein the track is an extensible and retractable track, one end of the track is inserted into the storage chamber, the other end of the track is arranged outside, and the microwave drying tank body is movably arranged on the track through electronic control wheels; and the storage chamber is of a splicing structure and is made of foam plates, one side or multiple sides of the storage chamber are provided with observation chambers, the storage chamber is provided with a rolling door, and the top of the storage chamber is provided with a ventilation opening. According to the automatic control storage system, the microwave drying tank body is movably arranged on the track through the electronic control wheels and enters the storage chamber to be stored when not used, the situation that the equipment is aged when the equipment is located outside is avoided, and meanwhile the cost is saved.