The invention discloses a matrix self-cleaning method in a CVD diamond deposition process and solves the problems of the prior art that the matrix cannot be cleaned completely and consequently nucleation is difficult, nucleation density is low and film forming quality is bad. The matrix self-cleaning method comprises the following steps: arranging the matrix and hot filament in a CVD vacuum deposition furnace, pumping air till ultimate vacuum, and introducing methane and hydrogen; lightening the hot filament; after the voltage of the hot filament is increased to a set value, observing the color change of the hot filament and the matrix; after lathe work is generated on the matrix surface, shutting off the methane, and reducing the hydrogen flow while introducing argon; when the lathe workon the matrix surface gradually disappears, the matrix color becomes bright red and the temperature sensor shows that the matrix temperature is between 600 DEG C and 900 DEG C, shutting off the argonand starting normal coating operation. The method disclosed by the invention is scientific and easy to operate, and can realize a matrix self-cleaning effect, increase the nucleation rate and improvethe film forming quality while creating a protective controllable reaction atmosphere.