Molecular dynamics simulation was used to examine the growth of methane hydrate in the presence of natural product pectin at different concentrations, including the mass fractions 2.46% and 3.62%. Snapshots of the system configurations with time, radial distribution functions of the carbon atoms, and the total energy of the system were employed to characterize the effect of pectin on methane hydrate growth. Results indicated that pectin is a good inhibitor of methane hydrate. The higher the concentration of pectin is, the better the effect of inhibition is. The double-bonded oxygen atoms of pectin combine with hydrogen atoms of water, and the hydrogen atoms of hydroxyl in pectin combine with oxygen atoms of water through hydrogen bonds, which disturbed the further growth of the methane hydrate. The role of the pectin’s active groups in hydrogen bonds with water both as proton donor and as electron acceptor makes pectin have a better inhibitory effect on the growth of methane hydrate.