The morphology evolution of thin films was studied by molecular dynamics simulation. In this simulation four deposition and substrate elements combinations were used: Al on Al(001), Al on Co(001), Co on Co(001), Co on Al(001). The Al thin film was always grown by layer-bylayer mode regardless of substrates used. On the other hand, thin films formed by Co deposition depended on substrates used.While Co thin films on the Co substrates were grown by the island mode, a 3 monolayer (ML) thickness of CoAl surface compound was initially formed on Al substrate, before pure Co thin film growth occurred. In addition to the study on morphologies, the degrees of mixing of atoms in the interface were studied quantitatively. No surface mixing and a sharp interface were observed when Co was used as a substrate regardless of deposited atoms. On the contrary, a large amount of surface mixing or compound formation was observed when Al was used as a substrate.