In a method of manufacturing a semiconductor device, a substrate is loaded to a process chamber having, unit process sections in which unit processes are performed, respectively. The unit processes are performed on the substrate independently from one another at the unit process sections under a respective process pressure. The substrate sequentially undergoes the unit processes at the respective unit process section of the process chamber. Cleaning processes are individually performed to the unit process sections, respectively, when the substrate is transferred from each of the unit process sections and no substrate is positioned at the unit process sections. Accordingly, the process defects of the process units may be sufficiently prevented and the operation period of the manufacturing apparatus is sufficiently elongated.