We have studied the effects of crystallinity on the emergence of porous morphology and strong green emission in ZnO thin films after H2 annealing treatment. The unique multiple-stacked porous structure is observed after performing H2 annealing treatment on the film with low crystallinity. However, the annealed high-crystallinity film exhibits surface morphology with a shallow porous structure, as revealed by SEM images. To study the effects of these unique porous structures on the optical properties, photoluminescence (PL) spectroscopy, Raman spectroscopy, spectroscopic ellipsometry, and X-ray photoelectron spectroscopy (XPS) are conducted. The multiple-stacked porous structure produces strong green emission as compared to the shallow porous structure centered at 2.5 eV, as detected by PL. Here, the green emission originates from the electronic transition related to the oxygen vacancy (VO). XPS spectra show that the high density of VO located on the multiple-stacked porous surface is much higher as compared to that for the shallow porous structure due to a high surface-to-volume ratio. The results show that the multiple-stacked porous structure has the potential to enhance the functionality of ZnO for applications in light-emitting.