Organic matter is a pivotal component in methane hydrate (MH) deposition and plays a crucial role in the MH formation process due to its intricate chain structures. In this study, organic matters (OMs) with varying carbon chain lengths, including glycine, alanine, phenylalanine, 12-amino dodecanoic acid, dodecyl amine, and dodecanoic acid, were selected to investigate their impacts on the kinetics, thermodynamics, and microstructure of MH. Kinetic experimental findings reveal that long carbon chain OMs and OMs containing hydrophobic functional groups promote MH formation, with a more pronounced effect at higher concentrations. Conversely, short carbon chain OMs and OMs with hydrophilic functional groups exhibit kinetic inhibition of MH. Thermodynamic experiments show that the effect of OMs on the thermodynamics of MH at low concentrations (<1 wt%) is negligible. At higher concentrations, 12-aminododecanoic acid and dodecyl amine at 5 wt% make the phase equilibrium conditions of MH more moderate, while glycine at 3 wt% shows an inhibiting effect. Furthermore, the interaction between OMs functional groups, water and methane molecules influences MH crystals, alters crystal size and increases the proportion of large and small cages of MH. This study is helpful for understand the role of OMs in MH formation, and promoting the in-depth understanding and application of MH resource occurrence and utilization.