The invention relates to a control system of the carbon intensity distribution of a low-pressure carburized layer and a control method thereof, belonging to the technical field of metal heat treatment. The control system comprises a low-pressure carburizing furnace, a controller, a pressure sensor, a thermoelectric couple, a nitrogen regulating valve, a nitrogen input pipe, a carburizing gas regulating valve, a carburizing gas input pipe, a vacuum system and a gas suction pipe. The invention simulates automatic optimized low-pressure pulse process parameters by using carburized layer concentration distribution values and realizes the control functions; the carburizing gas regulating valve executes on/off action according to an order of the controller to control carburizing section time and diffusing section time, therefore the accurate control of the intensity distribution of the carburized layer is realized; and in addition, the invention can keep high carburizing speed and prevent the tolerance of surface carbides, accurately controls the surface carbon intensity and the depth and the intensity distribution of the carburized layer, reduces the accumulated carbon black inside the low-pressure carburizing furnace, is free from depending on a gas component sensor and has the advantages of configuration simplification, easy implementation, high reliability and easy maintenance.