The process of mesophase formation of rodlike molecule, imogolite, was simulated by comparing the distance distribution function computed from models with that obtained by the Fourier-transformation of small angle X-ray scattering data. In the initial state below A-point (defined as a starting point of mesophase formation), imogolite molecules assemble into loosely packed hexagonal shape with their ends aligned in a line. The columns composed of hexagonal packing are arranged side by side to form raft-like sheets near the A-point and finally form mesophase above A-point.