A NiTi alloy root canal file with a flexibility gradient, having a tip, middle portion and rear portion divided along the longitudinal direction. The internal microstructure of the tip is martensite, of the rear portion is austenite, and of the middle portion is a combination of martensite and austenite. The microstructure of martensite is continuously reduced and the microstructure of austenite is continuously increased as the distance from the tip increases. A manufacturing method for the NiTi alloy root canal file with a flexibility gradient. As the internal microstructure of the NiTi alloy root canal file with a flexibility gradient gradually changes along the axial direction and the strength also gradually changes, the flexibility and strength show a gradient change along the axial direction of the root canal file, providing excellent cutting property, high anti-fatigue life and significantly improving operation performance, safety, and life of the root canal files.