Basing on the simplest hydrothermal system containing deionized water, hexa-ammonium molybdate, and thiourea, hydrothermal mechanism on preparation of MoS2 was studied by DFT calculation. Hydrothermal process was divided into four steps which covered ionization equilibrium, the hydrolysis of CS(NH2)2, the formation of intermediates, and the formation of MoS2. Ionization equilibrium occurs at normal condition and determines the existence of Mo in the form of molybdic acid. Thiourea hydrolysis is rate-determining step in the process of hydrothermal which contains 10 elementary reactions. The formation of intermediates includes hydrogen transfer, dehydration, and vulcanization three steps which contain 18 elementary reactions, and the energy barrier of vulcanization is the highest. The formation of MoS2 is divided into two steps, the first step is that MoO(OH)(SH)3.H2O reacts with MoO (SH)4.H2O to form layer MoS2, and the second step is a very fast process that can affect the morphology of the products.