We have investigated the effect of the interfacial interaction on the cross-sectional morphology of the tobacco mosaic virus (TMV) in solution and on two types of solid substrates, SiOx (polar) on Si(100) and polystyrene film (nonpolar) on Si(100), using small-angle X-ray scattering (SAXS) and grazing incidence small-angle X-ray scattering (GISAXS), respectively. Results reveal that the flexible chains at the outer surface of TMV either expand or contract depending on the nature of the substrate. Although the unfavorable interaction between the TMV and the PS causes a minimal effect, the stronger attractive interaction between the outer protein surface of TMV and the SiOx substrate induces pronounced deformation of its cross-sectional morphology.