Molecular dynamics (MD) simulation of the green ionic liquid [C₄mim][PF₆] mixed with polar benzonitrile (BNZ) solvent provides detailed insights into their structural and dynamic properties, essential for electrochemistry and materials science applications. The simulations we carried out at varying mole fractions (XBZN) reveal the mixtures’ physical, structural, and dynamic properties, with radial, spatial, and combined distribution functions, highlighting the effective interaction through H-bonding involved. The simulation indicates that BZN stacks on the cation butyl tail, providing a significant explanation for the unique experimental observations (following). Adding BZN causes the mixture’s liquid dynamics to increase linearly at low XBZN and exponentially at high XBZN, with a notable singular transition at 0.5XBZN. Comprehensive efforts were made to verify and support experimental sum frequency generation (SFG) spectroscopy by simulating the surface structure of the mixtures. Consequently, the simulated BZN stacking structure explains (1) the absence of the C≡N vibrational mode in the SFG spectrum for XBZN < 0.8, and (2) the gradual diminishing of the CH3 SFG signal, which disappears as XBZN approaches 0.5. Finally, this research removes a persistent ambiguity, proving that only the molecular moieties on the surface generate the SFG vibrational signal, while those in the subsurface do not.