Natural gas hydrate (NGH) is a highly promising alternative for gas storage and transportation. Nevertheless, the artificial generation of gas hydrates faces considerable obstacles for large-scale commercial implementation, primarily due to its slow formation rate and inadequate storage density. This study delves into the effects of gas to water ratios and metal nanoparticle dosages on the synthesis of NGH. Molecular dynamics (MD) simulations were employed to examine the formation of CH4 hydrate under varying gas to water ratios and metal nanoparticle concentrations. The investigation assessed critical parameters of the gas–water system, such as radial distribution function, carbon storage ratio, hydrate cages, potential energy, diffusion coefficient, and thermal conductivity. For the first time, Pearson's correlation coefficient analysis was utilized to discern the interrelationships among these factors. The results demonstrated that medium gas to water ratios led to increased carbon storage, a higher number of cages, and augmented energy consumption. The nano-Cu dosage impacted the stability of hydrates and the thermal conductivity of the gas–water system, particularly at elevated gas to water ratios. Drawing on the MD simulation findings, a design factor was introduced to appraise the performance of the multicomponent system, which in turn, informs the development of a high-performance NGH formation system. The effectiveness of the design factor was corroborated through laboratory experiments, revealing its robust potential for designing high-performance NGH systems. This research paves the way for the practical realization of efficient hydrate-based production in real-world applications.