Hydrogen gas accelerates hydrocarbon generation, but little is known about its distribution and origin in petroliferous basins, which has hindered the further exploration. Taken the Jiyang Depression in eastern China as an example, this study collected natural gas from different tectonic units, and analyzed various geochemical characters including gas contents, and carbon and hydrogen isotopic composition. The result shows that: (1) hydrogen gas is widespread distributed, but its content is very low, which typically ranges from 0.01% to 0.1% in this region; (2) the ratios of H2/3He, indicative of the origins of hydrogen gas, suggest that mantle-derived hydrogen is dominant. Even in tectonically stable areas absent with deep fluid activities, there is also mantle-derived; (3) the isotopic composition of hydrogen falls in the range of –798‰ to –628‰ (relative to VSMOW standard). In areas with deep-derived fluids, the hydrogen gas has a similar isotopic composition with the previously documented deep-sourced gas, with lighter isotopic composition. In contrast, hydrogen gas has a heavier isotopic composition in relatively stable areas. The isotopic signatures suggest that there is a mixture of mantle- and crust-derived hydrogen gas in the relatively stable area, which is consistent with the H2/3He ratios. Therefore, it is clear that the hydrogen gas has a much wider distribution than found in the deep-derived fluid area, resulting in a much broader area with hydrogenating effect for resource rock. This understanding will provide new insights for hydrocarbon generation research and resource assessment in petroliferous basins.