Today, a new biomedical application of various nanomaterials is the utilization of them as drug delivery systems (DDSs) for several anti-cancer medicines to decrease their problems by carrying them to the target tumor cell zone. In the recent project, we have studied the efficiency of the pristine BC2NNTs and functionalized BC2NNTs as a DDS for chlormethine (CM) anti-cancer drug applying the density functional theory B3LYP/6-31G (d, p). It was detected that CM interacted weakly with the pristine BC2N nanotubes (−13.60 kcal mol−1). Therefore, the functionalized BC2NNTs were studied for CM interaction. In comparison to pristine BC2NNTs, in the adsorption and stabilization of the investigated compounds as well as their thermodynamic energy, our computations revealed that H bonds between active positions of carboxyl functionalized BC2NNTs and CM were the key factors. The fractional charge transfer, molecular electrostatic potential, and natural bond orbital analyses showed a considerable charge transfer from CM drug to the functionalized BC2NNTs. In addition, it was discovered to be stable in aqueous environments with amounts for solvent energies, which is appropriate for CM drug delivery uses. This project proposes a novel plan to achieve a high-density CM drug on the BC2NNTs’ surfaces.