The biological degradation of organic wastes mostly generates biogas including CO2 and CH4. Since both gases may be utilized as feedstock for various industrial applications, the alternative of gas hydrates to separate or enrich such gas species is of particular interest. To promote the hydrate-based (HB) methods, introducing environmentally friendly promoters could either enhance the formation or improve the recovery rates. In this study, the effects of pure and binary organic amines (methylamine, dimethylamine, amylamine) and urea on the kinetics of CO2 + CH4 hydrate formation through molecular dynamics simulations were explored. To characterize the kinetics of biogas hydrate formation, different analyses such as the three/four-body structural order parameters, determination of hydrate-like cages, number of hydrogen bonds, molecular distributions, and energy variations were investigated. Results indicate that the promotion effects of organic molecules were evident in which the presence of methylamine, dimethylamine, and their mixture was found to be more kinetically efficient than other studied solution systems. These molecules can also induce guest gases toward being located inside the formed cages more than in pure water. Studied molecules can also affect the distribution of CO2 and CH4 molecules during the conversion of the solution phase to a clathrate-like state which could be a useful feature to intensify the split fraction of HB processes. Nonetheless, the addition of urea in either a pure or binary mixture with other amine molecules was not recognized as the observed efficiency of combined methylamine and dimethylamine. This investigation reveals the uncovered characteristics regarding the utilization of long/short-chain amines to upgrade the process of biogas separation through hydrate.