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Taking the Late Ordovician Wufeng Formation (WFF) shale in the Upper Yangtze region as an example, we conducted a lithofacies distribution, thickness quantification, and paleo-topographic reconstruction of the Late Ordovician graptolite zones. Specifically, we focused on the Late Katian Dicellograptus complexus and the Early Hirnantian Metabolograptus extraordinarius within a chronostratigraphic framework, using the Geographic Information System (GIS) and 310 stratigraphic sections (incl. drilling) obtained from the Geobiodiversity Database (GBDB). Reconstruction of the geographic distribution indicates that the WFF and the synchronous sediments in the Upper Yangtze region contain 8 litho-stratigraphic units, which are geographically distributed across 7 provinces/municipalities and do not exhibit significant variations in lithofacies. The black graptolite shale extends in a broad swath from east to west within the basin, while the other lithofacies deposited during the same period are present on the periphery of the basin. All these strata were deposited in a normal neritic epicontinental sea environment, except for the flysch sediments in the southern Hunan area. The thickness reconstruction involves a comparison of three spatial interpolation methods, including Inverse Distance Weighting (IDW), Kriging, and the Radial Basis Function (RBF). Based on a general verification, IDW is considered to be the optimal method since it has the minimum standard deviation and variance. Based on the contours obtained from the IDW model, the WFF black shale is estimated to have an overall area of 0.67 × 106 km2, an average thickness of 6.2 m, and a total volume of 3902 km3. This shale was deposited over a 2.83 Ma period. Therefore, the volume of shale deposited per million years is estimated to be 1379 km3/my and the average thickness of shale deposited per million years is 2.37 m/my. The Hirnantian paleo-water-depth values obtained using 275 sections were used to infer the Late Katian paleo-topography. These results suggest that the Yangtze platform was surrounded by ancient highlands to the west, south, and north, exhibiting a paleo-geographic framework characterized by one uplift and four depressions. This setting blocked water circulation, causing the water to be contained and forming a closed and restricted marine environment, which was one of the major factors controlling the deposition of the organic-rich WFF shale. With the advent of the big data era of geology, the methodology of GIS-based technology is readily exportable to any resource play having spatial distribution pattern. Results can be provided rapidly and efficiently generated from geological data.