During the Mesozoic, Southeast (SE) Asia (including South China and the South China Sea (SCS)) was located in a transitional area between the Tethyan and Pacific geotectonic regimes. However, it is unclear whether geodynamic processes in the SE Asian continental margin were controlled by Tethyan or paleo-Pacific Ocean subduction. Herein, we report ~124 Ma adakitic granodiorites and Nb-enriched basalts from the Xiaozhenzhu Seamount of the SCS. Granodiorites have relatively high Sr/Y (34.7–37.0) and (La/Yb)N (13.8–15.7) ratios, as well as low Y (9.67–9.90 μg/g) and Yb (0.93–0.94 μg/g) concentrations, typical of adakites. Their Sr/Y and (La/Yb)N values coupled with their relatively low initial 87Sr/86Sr ratios (0.70541–0.70551), relatively high K2O contents (3.31–3.38 wt%), high Th/La ratios (0.33–0.40), negative εNd(t) values (−3.62 to −3.52), and their variable zircon εHf(t) values (−3.8 to +5.2) indicate that these rocks were formed by melting of subducted oceanic crust and sediments. The Nb-enriched basalts show enrichment in high field strength elements (HFSE) and have εNd(t) values of +2.90 to +2.93, as well as relatively low initial 87Sr/86Sr ratios of 0.70341–0.70343, demonstrating that they were derived from a depleted-mantle (DM) source metasomatized by silicate magmas originating from melting of a subducted oceanic lithospheric slab. By combining our findings with data from other Late Mesozoic arc-related magmatic rocks and adakites from the broader study area, we propose a geotectonic model involving subduction of young oceanic lithosphere during the Late Jurassic and northward subduction of the proto-South China Sea (PSCS) along the SE Asian continental margin during the Early Cretaceous. This conceptual model better explains the two-period Mesozoic magmatism, commonly reported for the SE Asian continental margin.