The connecting structure of a center filler and a quarter member of a vehicle may include a lateral junction portion formed at a front end of the quarter member, the lateral junction portion coupling with one side surface of the center filler in a direction substantially perpendicular to a longitudinal direction of the vehicle. The connection structure may further include a longitudinal coupling portion formed in the longitudinal direction of the vehicle coupled with an outer quarter member of the quarter member, a trim coupling portion substantially the same length as the longitudinal coupling portion coupled with trim, and a connection portion connecting the longitudinal coupling portion and the trim coupling portion to each other, wherein the lateral junction portion extends at a front end of the longitudinal coupling portion, and the lateral junction portion is bent substantially perpendicular to contact to the center filler.