A pre-cleaning method of a substrate for a semiconductor device includes preparing a chamber, the chamber including a plasma electrode at an outside of the chamber, a power supplying system connected to the plasma electrode, a susceptor in the chamber, and an injector injecting gases into the chamber, equipping a metallic net in the chamber, the metallic net over the susceptor and grounded, disposing a substrate on the susceptor, and injecting a hydrogen gas into the chamber through the injector and supplying radio frequency power to the plasma electrode, thereby removing an oxide layer on the substrate.