Stiffened composite panels are often adopted for structural components of aircraft to avoid the buckling. For the design of stiffened composite panels, optimizations of both stacking sequences and cross-sectional geometry of panels are indispensable. In this paper, an efficient optimal design system of composite structures is proposed. We adopt Kriging method as approximation technique, and integrate it with a low-cost stacking sequence optimization method, the fractal branch and bound (FBB) method. The proposed method is applied to a minimum weight design of a hat-stiffened composite panel subject to a buckling constraint, and its high validity is confirmed.