The nanoporous carbon (NPC) performance, used for drug delivery carriers, wastewater treatment, or hydrogen storage, is strongly determined by the pore morphology during the desorption. In this work, the structural characteristics of NPC fabricated from rice husk by KOH activation were studied. X-ray diffractometry (XRD) and small-angle X-ray scatter were then implemented to characterize the pore size and adsorbate model under a series of adsorption–desorption conditions, combined with the details of the multilayer pore morphology obtained from gas adsorption. To this aim, the water was selected as adsorbate, which could be investigated under desorption conditions. The results confirmed that NPC changed from an amorphous structure to a regularly arrayed monolayer structure by introducing adsorbates and returns to their origin after thoroughly drying. A detailed understanding of the behavior of adsorbent and adsorbate may facilitate its storage ability and application in selective sorption, separation, and storage processes.