The invention belongs to the field of filament additive manufacturing, and discloses a polymer multi-material high-flexibility laser additive manufacturing system and a method thereof. The system comprises a first robot arm, a second robot arm, a positioner, a rotational extrusion nozzle in which a plurality of extrusion modules are disposed and a laser, each extrusion module is used for extruding one kind of filament, and the rotational extrusion nozzle is connected with the first robot which drives the rotational extrusion nozzle to move according to a preset trajectory; the laser is connected with the second robot, and is used for emitting a laser to fuse the filament extruded from the rotational extrusion nozzle, and through the cooperative motion of the first robot and the second robot, the extrusion and fusion of the filament are performed synchronously; the positioner serves as a forming mesa, and the rotation of the positioner cooperates with the motions of the two robots. With the present invention, problems such as easy blocking and short service life of the extrusion nozzle in the FDM forming are solved, thereby ensuring high flexibility of the manufacturing system and achieving the extrusion forming of the multi-material filaments.