The present technology provides a method of manufacturing a semiconductor device. The method includes forming a preliminary source structure, forming a stack structure on the preliminary source structure, the stack structure including a first material layer and a second material layer, forming a preliminary memory layer that penetrates the stack structure, forming a trench passing through the stack structure, forming a first buffer pattern by performing a surface treatment on a portion of the second material layer that is exposed by the trench, and forming a protective layer covering the first buffer pattern.