The invention discloses a furnace cleaning method for controlling the furnace bottom roller indentation of a thermal treatment furnace, which belongs to the technical field of cut deal thermal treatment. Before a steel plate is subjected to thermal treatment, the furnace temperature is raised to 600-700DEG C, a furnace cleaning plate of 80-100mm*3000-4000mm*10000mm is adopted and moves to a furnace tail from a furnace head at the speed of 20m/min (a specific numerical value or a numerical value range), stops advancing when reaching the furnace tail, and moves backwards to a furnace mouth; then, the steel plate is returned to be discharged out of the furnace; after the first piece of steel plate is discharged, a second piece of steel plate enters the furnace; a third piece of steel plate and a fourth piece of steel plate reversely move to the furnace head from the furnace tail with the same furnace cleaning mode; and four pieces of steel plates are adopted each time when the furnace is cleaned and are alternately used. The furnace cleaning method for controlling the furnace bottom indentation of the thermal treatment furnace has the advantages that the problem that the enterprise production period is severely affected due to blowing down and temperature reduction is solved.