The Tertiary in the West Depression Region of the Qaidam Basin has the typical inland salty lacustrine deposits in China. 34 natural gas samples were collected from 13 oil fields in the West Depression Region in the basin, the chemical compositions and carbon isotopes of methane, ethane, propane, and butane were measured. According to the carbon isotope characteristics of natural gases in combination with geochemical characteristics of the source rocks and crude oils, the natural gases can be divided into sapropelic associated gas, mixed organic matter-derived associated gas, coal-derived gas and mixed gas. The carbon isotope characteristics, origin and distribution of the natural gases are considered to be related with the types and distribution of organic inputs in lake environments with different salinities. The lake salinity can regionally forecast the distribution of the different genetic types of natural gas. Compared with the different genetic types of natural gas from other Chinese basins, the carbon isotopes of the heavy hydrocarbons of the natural gas from the Tertiary salt lacustrine facies in the Qaidam Basin are extremely heavier. Therefore, this should be considered when natural gases are genetically classified in the basin.