Methods of manufacturing a three-dimensional semiconductor device are provided. The method includes: forming a thin film structure, where first and second material layers of at least 2n (n is an integer more than 2) are alternately and repeatedly stacked, on a substrate; wherein the first material layer applies a stress in a range of about 0.1×109 dyne/cm2 to about 10×109 dyne/cm2 to the substrate and the second material layer applies a stress in a range of about −0.1×109 dyne/cm2 to about −10×109 dyne/cm2 to the substrate.