Controllable mining is a prerequisite for commercial hydrate mining and the addition of chemicals makes the mining process more efficient. However, traditional chemical additives are environmentally harmful and give rise to damage to the environment. Amino acids are green additives, and their effect on the decomposition of hydrates remains to be unequivocally understood. To reveal the influencing mechanism of amino acids on the decomposition of methane hydrates, molecular dynamics (MD) simulations were performed to systematically investigate the influences of the amino acid types, concentrations, temperature, and pressure on hydrates decomposition. The results demonstrated that glycine had shown excellent performance on accelerating the decomposition of hydrates, followed by valine, serine, alanine, and glutamic acid. 5 mol% glycine was most conducive to the decomposition of hydrates. Temperature was a favorable factor for the decomposition of methane hydrate, and the decomposition rate had a nonlinear relationship with the increase in temperature. Additionally, there were two factors affecting the decomposition of hydrates under varying pressure conditions. The first was the inhibition of pressure on the decomposition of hydrates, called inhibiting effect. The second was that pressure had an effect on the solubility of amino acids which could promote the decomposition of hydrates, called the facilitation effect. The synergistic effect of inhibiting effect and facilitation effect determined the final hydrate decomposition rate. The obtained results provided a qualitative and quantitative analysis of the decomposition process of the amino acid-hydrate system on the molecular scale, and also laid a basis for the selection and design of novel amino acid molecules promoting hydrates decomposition.