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The Qiongdongnan Basin (QDNB) is a rift basin located in the extension direction of the oceanic ridge of the Northwest Subbasin of the South China Sea. This basin is surrounded by Late Cenozoic Ocean Island Basalts (OIBs) magmatism associated with the putative Hainan mantle plume. However, how the Hainan mantle plume has affected the QDNB has not been studied in detail. To reveal the crustal structure of the QDNB and the possible influence of the Hainan mantle plume, we conducted a wide-angle seismic exploration from Hainan Island across the QDNB to the Xisha Block, and obtained the crustal structure by travel-time tomography. The results show that the crustal stretching factors of the Northern and Southern Rises of the QDNB are estimated to be 1.3–2.0, indicating slight or moderate crustal thinning. Whereas, the crustal stretching factor in the Central Depression of the QDNB is estimated to be more than 3.0, which means that the crust has been hyperextended. Controlled by two detachment faults (F2 and F11), the upper and lower crust show brittle and ductile thinning, respectively. Three anomalous low-velocity conduits penetrating the crystalline crust are developed in the Songnan Uplift and the Southern Rise of the QDNB. Their P-wave velocities are 5.5–6.0 km s−1, which are significantly lower than those of the surrounding crust (6.0–6.8 km s−1). The Late Cenozoic magmatic intrusions (e.g., sills and dikes) and hydrothermal activities can be observed in the sedimentary strata above these low-velocity conduits. We interpret that the low-velocity conduits might be the crustal magmatic footprints of the Hainan mantle plume, due to the correlated distributions of OIB-type magmatism, the magmatic intrusion patterns, the deep structure of the Hainan mantle plume and the high heat flow of 95 mW m−2. Thus, we propose that the crustal structure of the QDNB is the product of crustal hyperextension in the rifting stage and subsequently affected by the Hainan mantle plume magmatism. This study provides a typical case for understanding the influence of a mantle plume on the continental crust with pre-existing rift structures. [ABSTRACT FROM AUTHOR]