In order to recognize the impact of aqueous medium on gas yields and the kinetic behaviors of hydrogen isotope fractionation during organic matter thermal degradation, the gold tube apparatus was used to conduct thermal simulation experiments by mixing the nC18 with the water of different properties and proportions. The yields of natural gas components, the relation among hydrogen isotope composition of each component and the experimental temperatures vs. heating rates have been obtained, and the results indicate that under the higher temperature conditions, the hydrous experiment has obvious impact on gas yields, such as when more water is added, higher amounts of hydrocarbon gas and H2 are yielded, and the existence of water obviously prolongs the temperature interval with the existence of heavy hydrocarbon gas. It also shows that the hydrogen isotope of hydrocarbon gas generated by the hydrous experiment is obviously lighter than that generated by the anhydrous experiment, and with the increasing amount of added water, the δD value of hydrocarbon gas gradually decreases. Compared with gas yields, the variation of δD value is more sensitive to aqueous medium in the thermal simulation experiment. However, compared with the amount of the added water, the aqueous medium property has smaller impact on the gas yields, which still shows the inherit effect on hydrogen isotope composition of aqueous medium. Through the model simulation and the isotope fractionation behavior analysis, it is validated that the hydrogen isotope fractionation process can be well described by the chemical kinetic model. The difference of reaction fraction of normal methane and D-containing methane is large, corresponding to the same activation energy. The content of normal methane is obviously higher in the part with lower activation energy, while the content of D-containing methane is higher in the part with higher activation energy. Therefore, it will result in larger hydrogen isotope fractionation amplitude, and the δD values will be more sensitive to the variation of maturity. Meanwhile, the average activation energy of methane generation from nC18 in the hydrous experiment is higher than that in the anhydrous experiment, and the greater amount of added water, the larger the average activation energy of methane generation reaction. This has laid foundation for its exploratory application in the study of gas reservoir forming history and the gas-source correlation, which indicates the research and application prospects in this orientation.