A linear center rail structure for a sliding door includes a linear center rail, a roller part, a base, and an arm. The linear center rail is disposed on a side outer panel of a vehicle. The roller part is guided by the center rail, slid along the center rail, and has hinge holes formed at an end portion thereof. The base is fixed to a sliding door panel and has slots formed in a pop-up direction of the sliding door panel. The arm has one end at which a first hinge shaft rotatably coupled to the hinge holes of the roller part is disposed and the other end at which a second hinge shaft fitted into the slots of the base to thereby be slidably and rotatably coupled to the base is disposed.