The accretionary prism of the Hengchun Peninsula at the southernmost tip of the active Taiwan orogen has newly emerged due to the transition from a subduction zone to an arc‐continent collision zone. The mafic rocks within the Hengchun accretionary prism, whose provenance has long been controversial, are highly indicative of the mantle nature and tectonic evolution around the northern Manila Trench. Based on geochemical analyses, the accreted basalts are classified as normal and enriched mid‐ocean ridge basalts (N‐MORB and E‐MORB) and alkaline ocean island basalts. The N‐MORBs, which exhibit geochemical signatures indicative of virtually unmetasomatized depleted MORB mantle and yield zircon U‐Pb ages of 22.8 ± 0.3 and 24.2 ± 1.1 Ma, were off‐scraped from the subducted oceanic crust of the South China Sea (SCS). The alkaline ocean island basalts are considered fragments of subducted seamount due to their geochemical similarity with seamount basalts from the SCS. The Hf‐Nd isotopic compositions of basalts from the north SCS may represent the contributions of recycled oceanic crust and the upwelling Hainan Plume. The E‐MORBs, which exhibit similar geochemical compositions as rocks from the Huatung Basin and yield an 40Ar/39Ar age of 135.0 ± 5.6 Ma, were removed from the overriding plate due to the excessive shear stress between the converging plates and were laterally transported by strike‐slip movement; alternatively, they were off‐scraped from the subducted Luzon forearc slices. The temporary uplift and collapse of the accretionary prism caused by seamount subduction may have been responsible for the genesis of the lenticular Shihmen Conglomerate.