A theoretical study of polyaniline (PANI)/HNb3O8 layered nanocomposites has been performed based on ab initio calculations and experimental data. The Bronsted acidity of the layered niobic acid, and the interaction between the interlayered polyaniline molecules and the inorganic slabs in PANI/HNb3O8 nanocomposites, have been investigated. For the intercalation process of organic species into layered niobic acid, it is important to clarify whether the source of Bronsted acidity arises from the interlayered or hydrated protons. Thus, three inorganic layer structures, KNb3O8, HNb3O8, and HNb3O8 center dot H2O, are evaluated, and the results show that there is only a minor contribution to the total acidity if the hydrogen is tightly bound by the inorganic slab. After the interlayered aniline monomers are polymerized within the acidic inorganic layers, two orientated structures of PANI molecules are calculated in which the interlayered C6 rings are perpendicular and parallel to the inorganic slabs, respectively, based on the experimental results. In comparison, PANI molecules in the latter orientation are placed in a relatively narrower interlayer space, and the hydrated proton cannot simultaneously form two effective hydrogen bonds with the 0 atom of Nb3O8- and an N atom of the PANI molecule because of the orientation requirement of the hydrogen bond. The interlayered hydrated proton cannot effectively transfer electrons between the PANI molecule and the inorganic slab. A similar conclusion is also reached from a detailed analysis of band structure and density of states (DOS). The calculated results are in good agreement with the experimental fact that a relatively higher conductivity is apparent in the former rather than in the latter.