Following magma-poor continental rifting, the South China Sea (SCS) experienced seafloor spreading from ~33 Ma to ~15 Ma with an intervening southward ridge jump at ~25 Ma, generating the oceanic East, Northwest and Southwest Sub-basins. However, the magmatic processes during spreading remain poorly known owing to the lack of oceanic crustal images. Here we present a composite profile comprising three seismic lines that run from the northern continent-ocean transition (COT) to the extinct spreading center of the East Sub-basin to reveal the crustal structures. In the northernmost oceanic portion, the first oceanic crust featuring rough basement with numerous faults, and diffuse and weak Moho reflector, is only 3.9–4.5 km thick, implying relatively low magmatic budget and protracted tectonic extension continued from the magma-poor continental rifting to initial spreading. From the northern COT ocean-ward to the abandoned ridge where the jump event occurred, the basement becomes smooth with subdued faults. The Moho reflector tends to be continuous and strong, and the igneous crust gradually becomes thick (locally up to 8.4 km), suggesting considerably increasing magmatic budget during the early spreading stage. However, in the central portion spanning from the abandoned ridge to the extinct spreading axis, the basement becomes rough with crustal faults again. And the crust gradually becomes thin, to only 3.7 km at the extinct spreading center where a deep median valley is still visible, though severely altered by post-spreading volcanism, implying decreasing magmatic budget and increasing tectonic extension during the late spreading stage. Therefore, the crustal structure variations in the East Sub-basin reflects a prominent increasing to decreasing change of magmatic budget during spreading with the peak around the intervening ridge jump. Thin, tectonized crust and deep median valley around the extinct spreading center further support slow seafloor spreading during the last spreading stage of the SCS which ended at ~15–16 Ma, and also suggest that magma contribution from the Hainan mantle plume might be very limited if any.