Using X-ray reflectivity, we observe drastic differences in the interfacial structure and molecular ordering of diphenylsiloxane-dimethylsiloxane copolymer thin films deposited on hydroxylated versus H-terminated ( etched) silicon wafers. We find that substrate type and comonomer ratio determine the conformational arrangements in these liquid films. High-energy bonding between the substrate and the molecules and an increase in rigidity of the molecules due to replacement of methyl groups by phenyl groups leads to a specific molecular ordering at the liquid/solid interface and pronounced density oscillations in this region. The observed structural reorganizations are explained by the interplay and the established balance between the chain flexibility and the polymer-substrate interactions.