The invention discloses a flexible alloy rotary file cleaning tool and method for deep hole and intersecting hole burrs. The cleaning tool comprises a rotary rod and an alloy rotary file. The alloy rotary file is detachably mounted on an end portion of the rotary rod through a seat body. The rotary rod is hollow. The alloy rotary file is movably mounted on an end portion of the seat body through arotating shaft, so that the alloy rotary file can swing at least toward one side with respect to the rotary rod. A coolant passage is machined on the seat body. One end of the coolant passage is communicated with the inner hollow portion of the rotary rod. The other end of the coolant passage extends toward the alloy rotary file and opens toward the side surface of the alloy rotary file. The opening direction of the other end of the coolant passage is substantially perpendicular to the rotating shaft of the alloy rotary file. The design is relatively flexible and can meet the removal of burrsof holes of different sizes within a certain limit.