Abstract: Due to limited data on the geochemical properties of natural gas, estimations are needed for the effective gas source rock in evaluating gas potential. However, the pronounced heterogeneity of mudstones in lacustrine successions complicates the prediction of the presence and geochemical characteristics of gas source rocks. In this paper, the Liaohe Subbasin of Northeast China is used as an example to construct a practical methodology for locating effective gas source rocks in typical lacustrine basins. Three types of gas source rocks, microbial, oil-type, and coal-type, were distinguished according to the different genetic types of their natural gas. A practical three-dimensional geological model was developed, refined, and applied to determine the spatial distribution of the mudstones in the Western Depression of the Liaohe Subbasin and to describe the geochemical characteristics (the abundance, type, and maturation levels of the organic matter). Application of the model in the subbasin indicates that the sedimentary facies have led to heterogeneity in the mudstones, particularly with respect to organic matter types. The effective gas source rock model constructed for the Western Depression shows that the upper sequence (SQ2) of the Fourth member (Mbr 4) of the Eocene Shahejie Formation (Fm) and the lower and middle sequences (SQ3 and SQ4) of the Third member (Mbr 3) form the principal gas-generating interval. The total volume of effective gas source rocks is estimated to be 586 km3. The effective microbial, oil-type, and coal-type gas source rocks are primarily found in the shallow western slope, the central sags, and the eastern slope of the Western Depression, respectively. This study provides a practical approach for more accurately identifying the occurrence and geochemical characteristics of effective natural gas source rocks, enabling a precise quantitative estimation of natural gas reserves.