We present an in silico approach for modeling the noncovalent interactions between the human mitochondrial voltage-dependent anion channel (hVDAC1) and a family of single-walled carbon nanotubes (SWCNTs) with a defined pattern of topological vacancies ( v = 1-16), obtained by removing atoms from the SWCNT surface. The general results showed more stable docking interaction complexes (SWCNT-hVDAC1), with more negative Gibbs free energy of binding affinity values, and a strong dependence on the vacancy number ( R2 = 0.93) and vacancy formation energy ( R2 = 0.96). In addition, for most of the SWCNT vacancies that were analyzed, the interatomic distances for the interactions of the SWCNT-hVDAC1 complex with the functional catalytic residues (i.e., Pro7, Gln199, Gln182, Phe181, Val20, Asp19, Lys15, Gly14, Asp12, Ala11, and Arg18) that form the hVDAC1 active site (i.e., the voltage-sensing N-terminal α-helix segment) were very similar to or shorter than the interatomic distances of these residues for ATP-hVDAC1 interactions. In particular, the hVDAC1 residues that can be phosphorylated like Tyr10, Tyr198, and Se16 were significantly perturbed by the interactions with SWCNT with at least nine vacancies. In addition, the SWCNT vacancy family members can affect the flexibility properties of the hVDAC1 N-terminal α-helix segment inducing different patterns of local perturbations in inter-residue communication. Finally, vacancy quantitative structure-binding relationships (V-QSBRs) were unveiled for setting up a robust model that can predict the strength of docking interactions between SWCNTs with a specific topological vacancy and hVDAC1. The developed V-QSBR model classified properly all of the SWCNTs with a different number of SWCNT vacancies with exceptional sensitivity and specificity (both equal to 100%), indicating a strong potential to unequivocally predict the influence of SWCNT vacancies on the mitochondrial channel interactions.