Interfaces between a Si(110) substrate and 3C-SiC crystals grown hetero-epitaxially by CVD were investigated by cross-sectional transmission electron microscopy. Gas flow condition during the carbonization process affects the roughness of the substrate surface and there is an optimum condition to preserve the flat surface. High quality 3C-SiC crystals grew only on the flat substrate, with crystallographic relationship of Si[1-10]//SiC[1-10] and Si//SiC[1-1 - 2], because the well-lattice-match relationship was limited in a two-dimensional region at the SiC(111)/Si(110) interface. Using the optimum condition, some kinds of roughness at an atomic scale remained on the surface of the substrate. Nanoscopic observation of the crystals grown on an off-axis substrate revealed the influence of the roughness on the epitaxial growth and the defects generation at the interface.