The invention discloses a sewage treatment system and an application method thereof. The sewage treatment system comprises an anaerobic zone, an anoxic zone a, an aerobic area, an anoxic zone b and a membrane pool. The application method includes: firstly, placing an immobilized microorganism ball into the anaerobic zone, and then recycling prior to preparing the immobilized microorganism ball located at the bottom of the membrane pool, wherein period and size of a membrane component in indirect compression and recovery are regulated according to water flow rate in the membrane pool. The immobilized microorganism ball used in the sewage treatment system and the application method thereof is capable of keeping activity of microorganisms and separating sludge from water, and good settleability is achieved; by the aid of magnetic field, the immobilized microorganism ball can be kept in a state of suspension, and the activity of the microorganisms can be improved; the immobilized microorganism ball can be recycled, so that the microorganisms in the immobilized microorganism ball is always kept in a highly active state, sludge is difficult to be attached to the surface of a membrane through indirect compression and recover of the membrane component, and the sludge attached to the membrane component can be removed.