The invention discloses an aeration system of an MBR (Membrane Bio-Reactor) membrane module and a control method of the aeration system, and aims to solve the problem of easily-caused environment pollution or high aeration energy consumption or short service life of the MBR membrane module in the traditional aeration system of the MBR membrane module. The aeration system of the MBR membrane module comprises an MBR aeration manifold, an upper-layer aeration manifold, a lower-layer aeration manifold, a plurality of upper-layer aeration branch pipes and a plurality of lower-layer aeration branch pipes, wherein the MBR aeration manifold is arranged in an MBR tank; the upper-layer aeration manifold and the lower-layer aeration manifold are communicated with the MBR aeration manifold; the plurality of upper-layer aeration branch pipes are communicated with the upper-layer aeration manifold; the plurality of lower-layer aeration branch pipes are communicated with the lower-layer aeration manifold; the plurality of upper-layer aeration branch pipes are located on the same horizontal plane which is 400-450mm far away from the bottom of the MBR tank; the plurality of lower-layer aeration branch pipes are located on the same horizontal plane which is 150-250mm far away from the bottom of the MBR tank. The aeration system disclosed by the invention can be used for effectively controlling membrane pollution by using relatively low air flow.