In this study, the synthesis of silicon nanoparticles in a plasma system was investigated with a particular focus on the role of methane in the secondary plasma and its influence on the structural characteristics and temporal stability of the nanoparticles. Silicon nanoparticles were synthesized under two different conditions, namely with and without methane injection, and their structural evolution was analyzed immediately after synthesis and 20 minutes later using Raman spectroscopy (532 nm excitation) and Fourier-transform infrared spectroscopy (FTIR). Raman results revealed that nanoparticles synthesized under both conditions exhibit a nanocrystalline structure at the initial stage, as evidenced by the red-shift and broadening of the silicon optical phonon peak relative to bulk crystalline silicon, indicating pronounced phonon confinement effects. However, in the absence of methane, the Raman signature of silicon was significantly weakened after 20 minutes, whereas it was well preserved in the methane-assisted samples. These results indicate that methane plays a key role in surface chemistry engineering and significantly enhances the temporal stability of plasma-synthesized silicon nanoparticles, providing an efficient strategy for producing stable silicon nanomaterials for advanced applications.