Heteroepitaxial layers of 3C-SiC on Si(001) without antiphase domains (APDs), which can hardly be obtained by atmospheric pressure chemical Vapor deposition (APCVD), can be obtained by low-pressure chemical vapor deposition method (LPCVD) despite using on-axis Si(001) substrate. LPCVD is different from APCVD in the growth mode, i.e., three dimensional (3D) island growth in APCVD and step-flow growth in LPCVD. This difference is attributed to the difference of the main Si species to carry Si atoms onto the grown surface. Based on these results, we propose a new APD annihilation model taking account of the difference in the main Si species and the confirmation of this model is demonstrated by the cellar automata (CA) simulation.