Two-dimensional hexagonal mesoporous silica thin films of SBA-15 were synthesized on Si substrates via dip-coating using an evaporation-induced self-assembly process. The effect of the withdrawal speed on the thicknesses, one-dimensional pore alignments, and two-dimensional hexagonal pore arrays of the films was elucidated. Detailed analyses of FE-SEM and TEM images and XRD and XRR patterns of the synthesized thin films clarified that the pore sizes, interplanar spacings, and film thicknesses depend on the withdrawal speed. Furthermore, the same films were synthesized on Si substrates with microtrenches. The local flow of coating solutions around microtrenches affects the pore direction as well as the film thickness. In order to form well-ordered mesoporous silica thin films with large surface areas, it is important to control the synthetic conditions such as the local flow of the coating solutions as well as the physicochemical properties of the silica precursor solutions or template molecules.