Nano-porous palladium (Pd) thin films could potentially be applied to hydrogen gas sensing materials with high sensitivity and selectivity. In our previous study, a nano-porous Pd film was fabricated with a three-dimensional network structure from an AlPd mother alloy film by a dealloying method using the chelating ability of an organic acid. This process was simple and environmentally friendly because it only required organic acid in a ppm concentration, and did not exhaust a strong acid waste solution, including heavy metal ions. This method was modified to improve the Pd purity of the dealloyed specimen, reaction rate, and morphology control. In this study, the existence of a composition undulation pattern was shown in the AlPd mother alloy film, and its effects on the morphology of the dealloyed specimen were evaluated. Furthermore, this pattern could be controlled by N2 gas addition to the Ar sputtering gas during the preparation of the AlPd mother alloy film.