A memory system includes: a memory device including a three dimensional (3D) cell array, in which memory cells having the same height are coupled to a component word line by units of rows and component word lines having the same height are coupled to a group word line; and a controller suitable for controlling the memory device to perform a program operation with a program data into memory cells coupled to a data component word line selected from a plurality of component word line included in a single group word line and to perform a dummy program operation with dummy data into memory cells coupled to remaining dummy component word lines among the plurality of component word lines.