Flow separation can occur when a stratified flow passes over an obstacle. Previous studies concerning flow separation are mostly observed in the shallow water regions, e.g., fjord, driven by tidal flows. In this study, a novel view of flow separations of the intermediate water over the Hengchun Ridge and Ryukyu Arc off Taiwan is firstly reported using seismic oceanography by reprocessing the seismic data from two cruises 97306 and EW9509 in 2001 and 1995, respectively. Both seismic images show that water masses are separated by internal interfaces detached from sill crests. Over the Hengchun Ridge, it was previously considered that the intermediate water flowed out of the South China Sea into the Hengchun Trough. Flow separation occurred at the lee-side of the ridge forming a continuous interface > 15 km between the intermediate and deep water at 900 m depth. This interface suggests that (1) mean flow of the intermediate water always flowed eastward and (2) no lee wave was generated or radiated even during a spring ebb tide. Near the East Taiwan Channel, the only major passage of the Kuroshio into the Okinawa Trough, flow separation occurred when the Kuroshio intermediate water flowed over the Ryukyu Arc at 500 m depth. The separation interface is nearly horizontal and extends > 25 km from the sill break to the trough. Parameter estimations and morphologic comparisons show that both separation cases are neither boundary-layer separation nor post-wave separation. Model data from OFES (Ocean General Circulation Model For the Earth Simulator) reveal dense pools existing downstream of the sill crests. We propose that a density-forced flow separation mechanism could be responsible for the observed flow separations and absence of lee waves in this study.