Understanding the interactions between boron nitride-based nanocage scaffolds with drug molecules is a prerequisite for their application as drug carriers. Herein, the adsorption behaviors of the anti-fungal drug flucytosine (Fcy) on the surfaces of different zero-dimensional BnNn (n = 12, 16, 20, and 24) nanomaterials were systematically studied based on the density functional theory (DFT) and molecular dynamics (MD). An ideal complementarity between their electrostatic potential surface is witnessed for the most stable BnNn-Fcy complexes. The atoms in molecules (AIM) analysis further reveals the partially covalent B···N bond is the main force between Fcy and BnNn. And the interaction energy between the entities in both gas and aqueous phase diminishes with the increase of cage size. Meanwhile, significant reductions in the HOMO-LUMO band gap energy of BnNn-Fcy complexes were observed after Fcy adsorption. Furthermore, MD simulations demonstrate the spontaneous adsorption of Fcy molecules onto the surface of BnNn, with the adsorption capacity of BnNn decreasing as the cage sizes increase. The aforementioned findings collectively indicate the adsorption behavior of Fcy can be tailored by the selection of different BnNn, making it a potential candidate for Fcy drug delivery to meet different needs. Hopefully, the results would provide valuable theoretical guidance for the development of BnNn-based drug delivery systems. © 2023 Elsevier B.V.