Although zinc-based nanocomposites have good methylene blue (MeB) adsorption capabilities, their efficiency is heavily limited by pH. This is troubling because large-scale pH adjustment is not economically viable when treating huge volumes of MeB-polluted water. In this study, we eliminate this limitation by tuning the phase and pore structure of zinc hydroxide/zinc oxide (Zn(OH) 2 /ZnO) nanostructures to allow for interfacial pore-filling adsorption reactions that are pH-independent. The physicochemical optimization is achieved using different reaction temperatures and ammonium fluoride (NH 4 F) dopant concentrations under hydrothermal conditions. The phase and microstructure of the Zn(OH) 2 /ZnO nanostructures are characterized using ζ-potential, SEM, XPS, XRD, Tauc plots, FT-IR, and BET analysis. At 80 and 120 °C and without NH 4 F doping, λ-Zn(OH) 2 /ZnO nanosheets were generated with a high specific surface area and pore volume but low MeB removal capacity. However, the addition of NH 4 F creates solid and porous β-Zn(OH) 2 /ZnO polyhedrons with high activity. In particular, 120 °C and 1.0 g of NH 4 F produce highly porous β-Zn(OH) 2 /ZnO octahedral nanoparticles (i.e., 120-1) with a high concentration of 6-nm-sized pores, which were crucial for MeB interfacial pore-filling from pH 3 to pH 10. The adsorption kinetics is fast and governed by the Langmuir, pseudo-second-order, and intraparticle diffusion models. 120-1 can be immobilized on a chelating polymer such as polyacrylonitrile (PAN) to generate a flexible membrane with high performance. Our study shows that careful control of the pore structure and phase of Zn(OH) 2 in Zn(OH) 2 /ZnO nanostructures overcomes the pH limitations.