Abstract: To standardize the classification of engineering geological layers in Southern Jiangsu, improve the sharing efficiency of regional geological data, and strengthen the systematic understanding of regional geological conditions for engineering practice, this study focused on the demand for engineering geological work in the high-quality development of Southern Jiangsu. Based on the theoretical support of Quaternary geological research, a massive amount of geological data was systematically integrated. For the first time, an engineering geological layer division system covering the entire Southern Jiangsu was constructed. A total of 14 engineering geological layers and several sub-layers were identified and divided, effectively filling the gap in the unified division of engineering geological layers in the region. Particular emphasis was placed on representative soil layers that significantly affect construction safety, including clay layer, soft soil, liquefied sandy soil, and expansive soil in the Gehu Formation. The study revealed the complexity of the engineering geological structure closely related to engineering construction in the region. Based on the proposed stratification standards, geological data were generalized, and a high-precision 3D engineering geological structure model was constructed within a depth range of 200 m, which intuitively presents the spatial distribution of underground structures and provides a visual data foundation for the development and utilization of underground space. Furthermore, an engineering geological condition zoning system has been explored and formed, which is divided according to the principles of terrain and landform differences, rock and soil types and properties, distribution of important engineering geological layers, suitability of engineering construction, and geographical location. The strata were subdivided into three engineering geological zones, eight sub-zones, and several small zones, achieving a reasonable match between zoning results and engineering practice needs. This study provides key geological basis for the preparation of national spatial planning, demonstration of major project site selection, and precise prevention and control of geological safety risks in Southern Jiangsu, and have important practical value and guiding significance.