The invention relates to the technical field of seawater desalination, in particular to a seawater desalination system heat exchanger backwashing filter device and a backwashing method thereof, the IPC classification number is C02F, the seawater desalination system heat exchanger backwashing filter device comprises a frame body, an automatic control device, a heat exchange backwashing filter device, a heat source outlet pipe, a heat source inlet pipe and an auxiliary bypass, and the automatic control device is fixedly connected to the upper end of the frame body; the heat exchange backwashing and filtering device is mounted in the frame body; the heat source outlet pipe and the heat source inlet pipe are connected to one side of the frame body; the frame body comprises a supporting frame, an upper sliding guide rail, a lower sliding guide rail and a fixed end plate. According to the invention, safe and stable operation of the sea water desalination device can be effectively guaranteed, and flow channel blockage and disassembly cleaning frequency of the heat exchange backwashing filter device are reduced; the device has the advantages of being flexible to operate, high in automation degree, small in occupied area, high in heat exchange efficiency, good in backwashing effect, low in maintenance cost, stable in performance, wide in application, free of disassembly and cleaning, remarkable in comprehensive effect and the like.