To investigate the effect of particle-based hydrate inhibitors on hydrate crystallization, molecular dynamics (MD) simulations were performed at the interface of hydrate-forming liquids where 2 nm sized silica nanoparticles are stabilized. The hydrophobic nanoparticles were prepared by functionalization of CH3 groups on the amorphous SiO2 surface, and the three-phase contact angle of the oil (CH4 + decane), the aqueous phase (water + tetrahydrofuran (THF)), and the solid was 108.7 degrees. Although the hydrates were not crystallized on the solid substrate, there was a trend that hydrate nucleation occurred on the side of the aqueous phase in the presence of nanoparticles. Through the four-body structural order parameter profiles, the formation of a low order parameter layer around the nanoparticles was observed, which originates from the reduced diffusivity by water binding. Adjacent to this layer, an elevation of the order parameter appeared in the same region where nucleation occurs because the less ordered layer acts as nucleation seeds. Indeed, a well of low free energy is formed in the presence of nanoparticles, in contrast to the non-nanoparticle system where no significant deviations were observed. Also, the driving force of hydrate nucleation is reduced with the increased nanoparticle injection. The nanoparticles prevented the diffusion of methane into the aqueous phase, resulting in a V-shape graph of induction time and delayed hydrate growth rate. These simulation results on the nanoparticle effect will provide a fundamental basis for improving the performance of particle-based inhibitors.