Reducing greenhouse gas emissions by employing advanced porous adsorbents is critical for mitigating anthropogenic contributions to the climate change. In this study, molecular dynamics (MD) simulations were performed to investigate the adsorption performance of graphtriyne sheet as a potential methane adsorbent. A comparative analysis of two molecular representation models—united-atom and atomistic—was conducted using the Improved Lennard-Jones (ILJ) potential function. The results indicated that the united-atom model yielded a higher permeation rate and diffusion coefficient but exhibited lower gas uptake than the atomistic model. The lack of orientation effects in the united-atom model led to reduced steric hindrance, facilitating methane permeation; whereas the atomistic model’s stronger orientation effects lowered permeance. These findings highlight the significant influence of molecular representation on the accuracy of MD simulation results and emphasize the importance of selecting well-validated force field parameters for methane adsorption studies.