<p>The study aimed to accurately identify the unconformity between the Mesozoic Santai Formation and the Fangzi Formation in the Chengdao-Zhuanghai area of the Jiyang Depression, China, and clarify its structural characteristics. The study used comprehensive mud logging, well logging, seismic, and oil testing/production data. A combined approach of principal component analysis and Fisher discriminant analysis was adopted to identify the unconformity and its internal structure, followed by a systematic analysis of the structural characteristics of the unconformity and its influence on hydrocarbon migration. The results show that: (1) The unconformity between the Santai Formation and Fangzi Formation is a regional unconformity; (2) Rocks above the unconformity are dominated by mudstone, pebbly sandstone, and fine sandstone with poor physical properties, exhibiting low-amplitude anomalies in spontaneous potential and low acoustic transit time values. The weathered clay layer has a high shale content, low spontaneous potential values, and high acoustic transit time and natural gamma values. Semi-weathered rocks are mainly composed of mudstone, pebbly sandstone, and fine sandstone with high acoustic transit time values; (3) Vertically, the main lithological associations of the unconformity structure are mudstone-absence-mudstone and sandstone-absence-sandstone. Horizontally, rocks above the unconformity and semi-weathered rocks are widely distributed, while the weathered clay layer is scattered in patchy distributions; (4) Semi-weathered rocks can serve as channels for the short-distance lateral migration of hydrocarbons. This study proposes a method for identifying unconformities in complex tectonic settings, laying a foundation for more detailed exploration of unconformity-related hydrocarbon reservoirs.</p>