A hybrid computer numerical control (CNC) machining center and a machining method thereof are provided. The hybrid CNC machining center has at least a cutting tool head, a laser cladding tool head, a laser surface heat treatment tool head, and a computer numerical control unit. The cutting tool head, the laser cladding tool head, and the laser surface heat treatment tool head are alternately installed in a tool holder of the hybrid CNC machining center. Users can accomplish cutting, laser cladding, and laser surface heat treatment operations for a work-piece just in one single machine, so that the work-piece is unnecessary to be moved between different machines. Therefore, the steps and the process time of the machining operations are substantially simplified.