A method of manufacturing a semiconductor device is disclosed. The method may comprise: forming a gate stack on a substrate; depositing a first dielectric layer and a second dielectric layer sequentially on the substrate and the gate stack; and etching the second dielectric layer and the first dielectric layer sequentially with an etching gas containing helium to form a second spacer and a first spacer, respectively. According to the method disclosed herein, a dual-layer complex spacer configuration is achieved, and two etching operations where the etching gas comprises the helium gas are performed. As a result, it is possible to reduce damages to the substrate and also to reduce the process complexity. Further, it is possible to optimize a threshold voltage, effectively reduce an EOT, and enhance a gate control capability and a driving current.