Noncovalent functionalization of boron nitride nanotubes (BNNTs) in aqueous solution was achieved by means of pi-stacking of an anionic perylene derivative, through which carboxylate-functionalized BNNTs were prepared for the first time. Starting from the functionalized nanotubes, an innovation methodology was designed and demonstrated for the controlled near-surface carbon doping of BNNTs. As a result of such delicate doping. novel B-C-N/BN coaxial nanotubes have been fabricated, and their p-type semiconducting behaviors were elucidated through gate-dependent transport measurements.