A filter structure has a main body and a stirring member. The main body has a hollow containment space filled with a filtering material. A filtering mesh is disposed at a bottom side of the containment space. A first purifying opening is disposed at a top end of the main body. A second purifying opening is disposed at a lower sidewall position of the main body above the filtering mesh. A first cleaning opening and a second cleaning opening are disposed on the main body and respectively coupled to a first and second inner pipe. An outlet is disposed at a bottom of the main body. The stirring member has an upper cover corresponding to the first purifying opening of the main body. The upper cover further has a driving arm and a connecting rod, and the connecting rod has a plurality of stirring rods.