We use molecular dynamics (MD) simulations to examine the structural and dynamical properties of deep eutectic solvents (DESs)-based boron nitride nanotube (BNNT) nanofluid. The impacts of nanotube diameter on the physicochemical parameters of the systems under consideration are investigated. It is found that the addition of BNNT to DES increases viscosity as a result of a decrease in the diffusion coefficient of DES species. Similarly, increasing the diameter of the BNNT causes an increase in viscosity while reducing the diffusion coefficient of glycerol. The assessment of interaction energy and the number of hydrogen bonds rationalizes and explains these results. The density profile, radial distribution function, the number of hydrogen bonds, and orientation of two species are estimated to provide a molecular explanation of DES species behavior within and outside BNNTs. Our results reveal that the diameter of the BNNT influences the arrangement and number of DES species inside BNNTs. Except for the (8, 8) BNNT, where DES species are organized in a straight chain, the cylindrical structure of DES species is inferred inside all BNNTs. Likewise, various obtained physicochemical properties for glyceline are found in good agreement with experimental data. This new understanding of the DES-based nanofluids structure will help to understand the properties of these green novel solvents from the viewpoint of molecular scale in chemical processes, as well as suggest a powerful framework in solvent design applications.