The invention provides an online cleaning type aeration system and a cleaning method thereof. The online cleaning type aeration system comprises a blast aeration system, wherein the blast aeration system comprises a blower, an air main pipe and aeration units; the blower, the air main pipe and the aeration units are connected sequentially; each aeration unit comprises an air branch valve, a branchvertical pipe and a tank bottom aeration diffusion unit which is located at the bottom of an aeration tank, and the air branch valve, the branch vertical pipe and the tank bottom aeration diffusion unit are connected sequentially; the system further comprises gas stripping blowing systems and a chemical cleaning system; each gas stripping blowing system comprises a gas stripping pipe, a gas stripping valve and a filter tank which are connected sequentially, and is communicated with the corresponding aeration unit through the gas stripping pipe; the chemical cleaning system comprises a chemical box, a dosing pump, a flow meter, a ball valve and a check valve which are connected sequentially, is communicated with the aeration units through the check valve, and is started during blockage byinorganic dirt. According to the online cleaning type aeration system and the cleaning method thereof, purging and cleaning of the aeration units internally blocked by inorganic dirt can be performedwithout reducing water level or dismounting the tank bottom aeration diffusion units, and the biochemical aeration efficiency of the aeration tank can be recovered as soon as possible.