Three molecules HArF@BNNT(5,0), HArF@BNNT(6,0), and HArF@BNNT(7,0) have been formed by HArF encapsulated in boron nitride nanotubes (BNNTs) with different sizes. Due to the interaction between the HArF and the BNNTs, the HAr bond lengths are in a decrease trend, while the ArF bond lengths are in an increase trend compared with those of HArF. To investigate the nature of the interaction between H and Ar and the interaction between Ar and F, the quantum theory of “atoms in molecules” was carried out. The Laplacian (▿2ρb) values of HAr suggest that the covalent interaction plays a key role in the H-Ar interaction. For ArF, the results indicate that the Ar-F interaction has a dominant noncovalent character. Moreover, the results obtained from the ratio of the kinetic-energy density (Gb) and the potential-energy density (Vb) (−Gb/Vb) and the total energy density (Hb) are in good agreement with that of ▿2ρb values. In addition, the results of natural bond orbital charge and electron density difference between the HArF and BNNTs show that less electrons transfer away from the HArF to BNNTs with the gradual increase in the diameters of the BNNTs. © 2014 Wiley Periodicals, Inc.