A microorganism filter device for a fishpond and a filtering method thereof. The device comprises a first chamber, a first filtering material(7) provided in the first chamber, a water inlet(4) into the first chamber, a second chamber separated from the first chamber, a plurality of water channels(6) connecting the first chamber and the second chamber, a second filtering material(8) provided in the second chamber, and a water outlet(5) leaving the second chamber, wherein the first filtering material (7) and the second filtering material(8) are provided as a plurality of filler column and filler lumps respectively. Nitrification and reverse nitrification processes by the filtering media in the first filtering material(7) and the second filtering material(8), and then nitrogen is discharged into the air and the harmless nitrate is discharged back to the pond. The device has greater industrial application value.
