Introduction Microphase separated structure of block copolymer hin films has been analyzed by means of grazing incidence small angle X-ray scattering (GISAXS). In a thin film of block copolymers, the various structures have been reported to appear according to the film thickness, which are not predicted in a bulk sample with the same volume fraction. And it has been revealed that the orientation of the structure also depended on the thickness. We will report the thickness dependence on microphase separated structure of polystyrene-b-polyisoprene (SI) block copolymer which exhibits hexagonally packed cylindrical morphology in the bulk.