The invention provides a filter of a ventilation system, which comprises a filter unit and a control unit. A primary filter screen is installed behind a wind inlet blower, and a filter screen with fine meshes is arranged behind the primary filter screen; an HEPA high-density filter layer is arranged at an indoor wind inlet port, and a sealing baffle is arranged behind the HEPA high-density filterlayer; and the blower is a double-purpose blower, when the blower is used normally, the sealing baffle is in an open state, and when a wind inlet pipeline needs to be cleaned, the sealing baffle is closed by the control unit, and the blower is controlled for back suction, thus the dust accumulated on the filter screen can be cleaned. The invention has the obvious effects that by considering the phenomenon that dust accumulation can occur after a ventilated filter system is used for a long time, which causes certain influence on indoor environment, and the manual disassembly and cleaning of thefilter system are very complicated, thereby the back cleaning of the filter system can be realized at any time after arranging the double-purpose blower.