The invention discloses a glass substrate cleaning box, and relates to the technical field of cleaning of glass substrates. The glass substrate cleaning box can solve the technical problem that medical liquid is wasted. The cleaning box is a closed box body defined by a top face, a bottom face and side faces. A water inlet hole, a water outlet hole and an air exhaust hole are formed in the box body; and a partition board is fixedly arranged between two opposite inner side faces of the box body, and the box body is divided by the partition board into two cavities with communicating bottoms. According to the cleaning box in the embodiment, as bubbles cannot be discharged out of the box body along with gas, waste of the medical liquid can be effectively reduced, and the use time of the medical liquid is prolonged.