The Upper Ordovician Baota (Pagoda) Formation, a stratigraphic unit widely distributed on the Yangtze platform of South China, is marked by its abundant cephalopods and unique network structures throughout the formation. The water depth for the deposition of the Baota Formation, based on sedimentary structure and paleoecological qualitative analysis, has been a controversial topic for decades. Here, with abundant in situ cephalopod fossils collected from the Baota Formation in the Yaolongshan area of northern Guizhou, a quantitative bathymetry of the epeiric sea where the formation deposited has been interpreted from the coupling relationship between the septal strength index (SSI) of the cephalopods and their implosion depth. A total of 16 Sinoceras and 12 Michelinoceras specimens are selected for the SSI analysis, along with how external characteristics and internal structures is correlated with SSI, respectively. The result indicates that SSI shows significant positive correlations with external cone length and septal distance, but negative with the apical angle. Furthermore, SSI has little relationship to single internal structure, it is likely influenced jointly by multiple internal parameters. Additionally, the SSI values of Sinoceras and Michelinoceras range from 5.564 to 10.829 and 11.432 to 19.532, respectively, approximately equate to 128 to 169 m and 228 to 280 m of the actual depths. Obviously, although Sinoceras and Michelinoceras were often buried on the same bedding surface of the Pagoda network limestone, these two taxa had different ecological stratification in the water column and even different paleobiogeographic environment. Whilst intraspecific ecological stratification are unconspicuous within these two genera. Moreover, quantitative bathymetry of the epeiric sea based on the actual depths of Sinoceras and Michelinoceras show a deep water benthic environment (≥280 m) corresponding to the Baota Formation, which is much deeper than most previous speculations.