Si thin epitaxial layers were grown by a temperature modulation Si molecular-layer epitaxy (TM Si MLE) method using Si2H6 gas. The surface was observed by the use of a high-resolution field-emission scanning electron microscope (FE-SEM). The surface morphology changed drastically from a three-dimensional island feature to a two-dimensional flat surface with lowering of the modulated temperature from 530 degreesC to 460 degreesC. In conjunction with the result of the in situ observation of the surface hydrogen desorption reaction, the mechanism of the change in the surface morphology was examined.