Complex structural geology generally leads to significant consequences for hydrocarbon reservoir exploration that needs a comprehensive methodology for complete comprehension. Despite a large number of existing wells in the Kadanwari field, Middle Indus Basin (MIB), southeastern Pakistan, the depositional environment of the Early Cretaceous stratigraphic sequence is still poorly understood, which has implications for regional geology as well as economic significance. To improve the understanding of depositional environment of complex heterogeneous reservoirs with associated 3D stratigraphic architecture, spatial distribution of facies and properties, and hydrocarbon prospects, a new methodology of three-dimensional structural modeling (3D SM) and joint geophysical characterization (JGC) is introduced in this research. JGC makes use of seismic interpretation-aided 3D SM, 3D seismic attributes analysis coupled with petrophysical modeling using 3D seismic reflection, and borehole data. Subsequently, the 3D SM reveals that the Kadanwari field experienced multiple stages of complex deformation dominated by NW to SW normal fault system, high relief horsts, half-graben, and graben structures. 3D SM and 3D fault system models (FSMs) further depict that the middle part of the sequence experienced more deformation compared to the surroundings of major faults with predominant oriented in S30°-45°E and N25°-35°W, azimuth as 148°–170° and 318°–345°, minimum (28°), mean (62°), and maximum (90°) dip angles. The applied variance edge attribute better portrays the inconsistency of the seismic data associated with faulting and estimated high reflection sediments presumed to be potential hydrocarbon traps. The high amplitude and loss of frequency anomalies of sweetness and root mean square (RMS) amplitude attributes represent cleaner and payable sand-rich shoreward facies revealing gas saturated sand, while relatively low amplitude and high-frequency anomalies indicate sandy shale, shale, and pro-delta facies, unfavorable zones for gas potential. The quantitative petrophysical modeling result shows that E sand interval has good effective porosity (∅ eff ) and hydrocarbon saturation (S hc ) compared to G sand interval. The derived average petrophysical properties, such as volume of shale (V shale ), average porosity (∅ avg ), ∅ eff , water saturation (S W ), and S hc of the E sand interval are 30.5%, 17.4%, 12.2%, 33.2%, 70.01%, respectively. The newly introduced 3D SM and JGC workflow is an effective tool for highlighting potential areas of high quality reservoir development.