The Osaka Bay is situated at a seismically active region north of the Median Tectonic Line and east of Awaji Island in western Japan, known as part of the Kinki Triangle and the Niigata–Kobe Tectonic Zone. Dense distribution of active faults and high geodetic strain rates characterize the region, posing a major seismic hazard potential to the coastal and metropolitan areas of the Kansai region. To investigate the shallow structure and recent deformation history of active faults in the Osaka Bay, we acquired 15 high-resolution seismic profiles using a Mini-GI airgun and a Boomer as active sources, together with multi-beam bathymetry data across the Osaka Bay Fault. Our seismic sections image a ~ 0.1 to 3.7 km-wide asymmetric anticline forelimb above the Osaka Bay Fault at shallow depths, coupled with a ~ 2.6 km-wide syncline to the west, and a broad, ~ 11 km-wide syncline in the footwall to the east. The synclinal axial surface at shallow depths measured in this study ranges 75°–89°. We observe the vertical displacement of the Osaka Bay Fault increasing northwards along strike. The sediment thickness on the hanging wall, however, is variable, modified by non-tectonic processes such as by tidal currents, affecting the geometry of growth strata. The most recent deformation by the Osaka Bay Fault reaches to near the seafloor by active folding, with large vertical offsets of 8–14 m over the last ~ 11 ka, and 5–11 m over the last ~ 5 ka. By combining with previously reported borehole age data, the average uplift rate on the Osaka Bay Fault is estimated to be ~ 1.0 to 1.7 m/ka during the Latest Pleistocene to Holocene. The inferred slip of the Osaka Bay Fault during the Holocene is likely to account for > 5% of the regional geodetic strain accumulation within the Kinki Triangle. Further studies to evaluate the Holocene slip rates of regional faults are necessary to assess the seismic hazards and the internal strain budgets within the Kinki Triangle and the Niigata–Kobe Tectonic Zone.Graphical abstract