The invention relates to an intelligent colony counting incubator and a counting method. The intelligent colony counting incubator comprises a computer assembly, an imaging assembly, a mechanical arm,a culture utensil station, a heating pipe, a recovery assembly, a horizontal bottom plate, a box inlet assembly and a door opening and closing assembly, wherein the computer assembly is in sliding connection with a stand column; the imaging assembly is fixedly connected to the bottom plate in the incubator; the mechanical arm is fixedly connected with the horizontal bottom plate; the culture utensil station is semi-annular, and is fixedly connected with the horizontal bottom plate; the recovery assembly consists of a box outlet part and a recovery part, wherein the box outlet part is fixedlyconnected to the horizontal bottom plate; the recovery part is fixedly connected to the outer side of the box body; the box inlet assembly is fixedly connected with the horizontal bottom plate; and the door opening and closing assembly is fixedly connected to the front inner wall surface of the box body. The intelligent colony counting incubator disclosed by the invention is simple in mechanical structure and reasonable in layout, automation of colony culture, colony imaging counting and colony recovery can be realized, labor is saved, efficiency is improved, cost is reduced, and the intelligent colony counting incubator has important significance in development of colony culture.