Due to the scarcity and uneven distribution of data, as well as the complexity of geological conditions, high-precision 3D hydrogeological structure modeling, especially at large scales, remains a significant challenge in the field. To address this issue, this study undertakes an in-depth analysis of the correlation between stratigraphic and hydrogeological structures. Utilizing the cumulative thickness of various aquifer types as a criterion, we establish a quantitative correlation model between stratigraphic and hydrogeological structures. This innovative approach transforms the task of 3D hydrogeological structure modeling into 3D geological structure modeling, where data are relatively abundant, thereby overcoming the data scarcity problem. To demonstrate the scientificity and feasibility of our approach, we utilize the 3D hydrogeological structures modeling of Wuhan’s metropolitan development area (MDA) as a case study. This study provides a quantitative criterion for the correlation between stratigraphic and hydrogeological structures, addressing the subjectivity and arbitrariness of previous qualitative evaluations. Additionally, it offers a scientific solution to the data scarcity issue commonly encountered in 3D hydrogeological structure modeling. Consequently, this study holds significant scientific value and practical implications.