Passive margins are first-order tectonic features on earth, formed by polyphase extension and breakup of continental lithosphere. It is accepted that mildly extended basins in the proximal margin form largely by uniform continental thinning, but the continental extension in deepwater is much debated. Here we choose a line from the western Qiongdongnan Basin in the magma-poor South China Sea margin to further explore the style of continental extension and the corresponding subsidence patterns, where high resolution seismic and heat flow data are available. Structural analysis reveals that the basin architecture is extremely asymmetric and mainly controlled by the SE directed normal faults, soling into a low-angle detachment fault. However, fault timings nicely show that the faults form through polyphase rifting and from inside outwards, and do not follow a simple sequential faulting like the West Iberia margin, where the upper and lower crustal deformation are strongly coupled. Perhaps the fault order here reflects a much weaker and decoupled lower crust. Then we divide the basin into five zones and calculate the average fault derived extension factors. Moreover, the whole crustal extension factors are also estimated after assessing the initial crustal thickness on basis of the backstripped subsidence. And the lithospheric extension factors are numerically modeled using a coupled lithosphere and basin scale model constrained by the heat flow and sedimentation data. Results show that along the profile, the overall lithospheric extension is much less than that of the whole crust, and only at the south end of the profile does lithospheric extension exceeds the whole crust, showing lithospheric depth-dependent thinning. The whole crustal extension is roughly equal to the faults derived extension in the northern part, displaying no extension discrepancy. In the middle part, the whole crustal extension is less than the faults derived extension, denoting inverse extension discrepancy. While the whole crustal extension is in far excess of the faults derived extension in the southern part, showing obvious positive extension discrepancy. We infer that the inverse and positive discrepancy of crustal extension was likely to be caused by landward directed lower crustal flow, driven by the horizontal pressure arising from the combination of the differential extension in the faulted upper crust, in the mantle lithosphere, and the differential sedimentation during the syn-rift period.