Provided is a segment-block-based handwritten signature authentication system and a method thereof, and more particularly, to a handwritten signature authentication system and a method thereof that enrolls a handwritten signature including handwritten signature characteristics information based on segment blocks disjointed by a user, acquires segment-block-based handwritten signature characteristics information from the handwritten signature upon request for handwritten signature authentication, and performs handwritten signature authentication by comparing the pre-enrolled handwritten signature characteristics information based on segments and the acquired handwritten signature characteristics information.