A hybrid bio actuator and a manufacturing method thereof using a 3-dimensional micro molding aligning apparatus are provided. The manufacturing method has the steps of: 3-dimensionally forming an actuator body with polymer using the micro molding aligning apparatus; and transplanting and cultivating the muscular cell onto the actuator body. The step of forming the actuator body comprise: preparing the upper and lower half molds corresponding to an outer contour of the actuator; installing, on the mold plate unit, the upper and lower half molds opposite to each other and placing a mass of polymer above the lower half mold; aligning the lower half mold with the upper half mold using the aligner unit; pressing the mold plate unit using the clamp unit; solidifying the polymer; and removing the solidified polymer, thereby providing the hybrid bio actuator made of a biomaterial compatible with the human body and capable of operating without a separate battery or external energy source.