Recently, there has been significant interest in the synthesis and potential applications of semiconductor nanotubes (NTs). In this context, many efforts have been invested in developing new routes to control and engineer their surface chemistry. We report herein on a simple route to differentially and selectively functionalize the inner and outer surfaces of silicon nanotubes (SiNTs) with organic molecular layers containing different functional groups and hydrophobicity/hydrophilicity chemical nature, via covalent binding, to give nanotubular structures with dual chemical properties. Significantly, our unique synthetic approach can be further extended to directly form hollow crystalline nanotubular structures with their inner/outer surfaces independently and selectively altered chemically. Additionally, SiNTs inner and/or outer walls can be selectively decorated with metal nanoparticles. Both inner and outer walls can be individually and separately modified with the same metal nanoparticles, with different metal NPs in the inside and outside walls or with a combination of metal NPs decoration and molecular layers, if so required. Furthermore, the dually modified nanotubes were then exploited as phase extraction nanocarriers to demonstrate their potential in future chemical and biological separation, extraction, and filtering applications.