The invention discloses a clamping alignment device for transmission shaft groove processing and a using method. The clamping alignment device comprises a cover plate (2), an inner adjusting screw (4), a square box (5), a pressing plate (6), a pressing plate screw (7), pressing plate supporting rods (8), an outer adjusting screw (10) and a fastening pin (11), the cover plate (2) is mounted on thesquare box (5), a V-shaped through hole (21) is formed in the middle of the cover plate (2), the end of the inner adjusting screw (4) after penetrating in from one side of the cover plate (2) penetrates out from the side wall of the V-shaped through hole (21), and the outer adjusting screw (10) is mounted at the edge of the upper surface of the cover plate (2) and positioned on the opposite side of the inner adjusting screw (4); the pressing plate supporting rods (8) are symmetrically mounted on two sides of the V-shaped through hole (21), the pressing plate (6) is mounted on the pressing plate supporting rods (8), and the pressing plate screw (7) after penetrating the pressing plate (6) is mounted on the cover plate (2). The clamping alignment device enables a common milling machine to process a transmission shaft groove, so that an expensive multiaxis processing center is not needed.