The atomic arrangement and bonding characteristics of void-free 3C-SiC/Si(100) grown by the modified four-step method are presented. Without the diffusion step, Si–C bonds are partially formed in the as-carburized layer on Si(100). The ratio of C–C bonds to Si–C bonds is about 7:3, which can be lowered to about 1:9 after the diffusion step at 1350°C for 5 min or at 1300°C for 7 min according to C 1s core level spectra. The residual C–C bonds cannot be removed, which is associated with an irregular atomic arrangement (amorphous) located either at the 3C-SiC/Si(100) interface or at the intersection of twin boundaries in the 3C-SiC buffer layer based on the lattice image taken by transmission electron microscope. The diffusion step helps the formation of Si–C bonds more completely and results in a SiC buffer layer of high quality formed on Si(100) before the growth step. However, twins and stacking faults still appear in the 3C-SiC buffer layer after the diffusion step. The formation mechanism of the 3C-SiC buffer layer is proposed and discussed.