Sichuan Basin is one of the structurally stable and gas-rich basins, being regarded as one of China’s important natural gas industry bases. Puguang and Jiannan gas fields, located in the eastern Sichuan Basin are two large fields with gas derived from Permian and Lower Triassic marine carbonate. The genesis of marine carbonate natural gas was examined using carbon isotope composition and hydrocarbon components of natural gas samples from the eastern and western Sichuan Basin, and compared with that of acidolysis gas derived from marine source rock in the eastern Sichuan Basin. It is concluded that the natural gas in the marine carbonate reservoir originated from pyrolysis of the earlier crude oil and light-oil, and then mixed with kerogen pyrolysis gas of the Permian and Lower Silurian source rock.