An efficient and environment friendly surface-protected etching method by using mesoporous silica as a template and alkaline polyelectrolyte as both the protecting and etching agent was developed to prepare a SiO2 nanotube with a porous shell. The polyelectrolytes attached to the template not only create a localized alkaline environment, but also effectively protect the silica surface, whereas the mesopore channels accelerate the diffusion of etchant throughout the template, all of which facilitate the formation of hollow structures in a fully controllable way. By tuning the etching power and protecting ability of the polyelectrolyte, the rigidity and porosity of products can be precisely manipulated. It is inspiring that various alkaline polyelectrolytes including polypeptide and dextran derivative can be used for the etching process, so that the porous and hollow nanostructures are born with positively charged and biocompatible surface as well as abundant amino groups for further coupling, which make them potential capsules for drug delivery and probes for imaging and detection. The protective etching process can also be extended to the preparation of yolk-shell super structures with functional cores, or porous nanoparticle assemblies with their individual characteristics maintained.