Introducing wrinkling or rough features into substrates is of great practical significance to construct various functional surfaces. Due to the sensitivity of assembled units towards environmental stimuli, the internals of layer-by-layer films can be readily adjusted to generate various micro- and nanostructures. We previously described a self-roughening polyelectrolyte multilayer (PEM) to facilitate the introduction of surface microstructures. In the present work, the growth process of PEI/PAA multilayer films was investigated and the mean size of the surface microstructures was found to increase linearly with the film thickness. The spontaneous formation of these surface features can be attributed to swelling-induced film deformation during the assembling process, which is similar to the surface wrinkling of hydrogels undergoing a volume phase transition. When exposed to saturated humidity, the internal stress as well as the surface microstructures can be diminished spontaneously, leading to a flat surface over the substrates. Given the effect of the underlying film thickness on the characteristic wavelength of the surface wrinkles, multiscale surface microstructures can be readily realized by means of spatially presetting the distribution of the film thickness.