Natural Deep Eutectic Solvents (NADES) are emerging as sustainable alternatives to conventional organic solvents and ionic liquids, with promising applications in extraction, biocatalysis, and pharmaceutical formulation. However, the rational design of these solvents remains challenging due to the complex role that hydrogen bonding plays in determining their physicochemical properties. This study uses molecular dynamics simulations to obtain and correlate hydrogen bonding metrics—total hydrogen count, donor-acceptor distance, and bond angle—with five key properties in Type V NADES: solubility, viscosity, density, melting point and boiling point. Seven thymol–menthol (Thy-Men) and menthol–lauric acid systems (Men-Lau) were simulated using GROMACS at various molar ratios. Results show that stronger hydrogen bonding increases solubility, density, and boiling point while depressing viscosity and melting point. Highest number of hydrogen bond, NHB were observed in the Men-Lau (0.5:1) and Thy-Men (2:1) systems, reaching 124.921 and 114.178, respectively. This work establishes hydrogen bonding as a predictive design parameter, enabling the tailored formulation of NADES for green chemistry applications.