IODP Hole U1502B penetrates >180 m into the crystalline basement generated at a rifting margin of the South China Sea (SCS), which is the first confirmed intermediate-type margin worldwide. The recovered lavas show petrographic characteristics of mid-ocean ridge basalt (MORB), but suffered pervasively from hydrothermal alteration. This sequence represents the oldest SCS oceanic crust ever drilled in-situ, and offers a globally unique window to explore the hydrothermal processes during continental breakup. Here, 50 whole-rock samples representative of Hole U1502B were analyzed for major & trace elements and Sr–Nd isotopes, presenting the first report of hydrothermally altered basalts for the SCS. The protolith appears to be tholeiite, enriched MORB, and little affected by crustal contamination due to the constant mantle-values of ε_Nd. However, the altered rocks are characterized by significant Ca depletion and ⁸⁷Sr/⁸⁶Sr modification. Major processes are identified to be tightly involved with plagioclase: chloritization and albitization. Both reactions are responsible for the Ca-loss and Sr-mobility, and for the resultant Mg- and Na-uptakes, respectively. Environments varying from the peripheral to deep parts within a discharge zone are evidenced by the co-existence of hydro-fracturing brecciation, high water/rock ratios (~1–25), and lower greenschist facies alteration (albite–chlorite–epidote + quartz). This variability can be attributed to detachment-related faulting, which provides permeability allowing deeply channeled pathways of fluids. Such tectonic effects also permit a penetration of Hole U1502B into the lava–dike transition. With a migration from on-axis to off-axis alterations discerned, our results together imply a more complex and longer SCS rifting than previously thought.