In order to discuss the role and influence of water during the generation of natural gas, the participation mechanism of water during the evolution of organic matter and its influences were summarized. In addition, we carried out an anhydrous cracking experiment of oil extracted from the Feixianguan Formation source rock in a closed system, which led to the establishment of the kinetic models for describing carbon and hydrogen isotopic fractionation during gas generation from organic matter. The models were calibrated and then applied to the northeastern Sichuan Basin. By combining a series of gas generation experiments from octadecane pyrolysis without water or with distilled water in varying mass proportions, several results were proved: (1) the hydrogen isotopic composition of natural gas becomes lighter with the participation of formation water; (2) we can quantitatively study the hydrogen isotopic fractionation with the kinetic model for describing carbon isotopic fractionation; (3) more abundant and reliable geological information can be obtained through the combined application of carbon and hydrogen isotopic indices.