Scanning tunneling microscopy has been used to investigate the adsorption of C60 molecules on Si(100)‐(2×1) surfaces at various deposition temperatures. At room temperature, submonolayers of C60 molecules experienced limited surface diffusion and randomly adsorbed to sites between dimer rows. At 650 °C, the C60 exhibited increased diffusion and preferentially adhered to step edges, and defects, or bonded to the top of the dimer rows. At low coverage, a strong interaction between the C60 and Si was evidenced by increased defect density which included the local atomic rearrangement in the vicinity of the C60 molecules. Higher coverage created a substantial concentration of defects which induced Si(100)‐c(4×4) reconstruction. At 750 °C, the C60 molecules decompose and react with the Si surface forming islands of SiC and C60–Six species.