A closed-in compartment air cleaning system and a control method thereof are disclosed, wherein the system id composed of three subsystems: a main air cleaning system, namely called as the adsorbing air cleaning system; a vice air cleaning system, namely called as the catalytic combustion air cleaning system; a linking combinatorial system, also called as the desorption reproduction system, having the advantages of combining the adsorption, the desorption, the catalytic combustion, to integrate the closed-in compartment air cleaning perfect system. The system adopts PLC microcomputer planed as a whole to control each link, which is of high efficiency, energy saving, environmental protection and sanitation. The air cleaning system and the control method can be designed into the air cleaning device with different specification according to the requirement, which can be used in the nuclear submarine, the AIP submarine, the conventional submarine, the manned spacecraft, the underground anti-aircraft defense and the air cleaning process of the air standard plant, and is an ideal closed-in compartment air cleaning system and a control method.