The invention discloses a preparation method and an application method of a membrane pollution inhibitor for a membrane bioreactor. The preparation comprises the following steps: respectively preparing a sodium alga acid solution, an allicin solution and a brominated furanone ethanol solution of different mass percents; dripping the solution into a calcium chloride solution, forming microspheres containing the membrane pollution inhibitor, performing suction filtration, and performing freeze drying. During specific application, the microspheres subjected to freeze drying are added into the membrane bioreactor at a time, wherein the mass concentration ratio of the addition amount to sludge concentration is 1:(50-70). According to the membrane pollution inhibitor, communication among dominant signal molecules in the membrane bioreactor can be effectively blocked, so that target genes cannot be expressed, and biological membrane formation is inhibited. The concentration of microbial metabolism products in the reactor can be obviously reduced, the membrane pollution rate is obviously reduced, the microbial growth rate is reduced, the activated sludge concentration is reduced, and the sludge treatment cost is reduced. Moreover, the preparation method and application method of the membrane pollution inhibitor have the advantages of simplicity in operation, low cost, reliability in operation, zero secondary pollution and the like.