Provenance studies of the Central Canyon, Qiongdongnan Basin has provided significant insights into paleographic and sedimentology research of the South China Sea (SCS). A suite of geochemical approaches mainly including rare earth elemental (REE) analysis and detrital zircon U–Pb dating has been systematically applied to the “source-to-sink” system involving our upper Miocene–Pliocene Central Canyon sediments and surrounding potential source areas. Based on samples tracing the entire course of the Central Canyon, REE distribution patterns indicate that the western channel was generally characterized by positive Eu anomalies in larger proportion, in contrast to the dominance of negative values of its eastern side during late Miocene–Pliocene. Additionally, for the whole canyon and farther regions of Qiongdongnan Basin, the number of samples bearing negative Eu anomalies tended to increase within younger geological strata. On the other hand, U–Pb geochronology results suggest a wide Proterozoic to Mesozoic age range with peak complexity in Yanshanian, Indosinian, Caledonian and Jinningian periods. However in detail, age combination of most western samples displayed older-age signatures than the eastern. To make it more evidently, western boreholes of the Central Canyon are mainly characterized with confined Indosinian and Caledonian clusters which show great comparability with mafic-to-ultramafic source of Kontum Massif of Central Vietnam, while eastern samples largely bear with distinguishable Yanshanian and Indosinian peaks which more resemble with Hainan Island. Based on geochemistry and geochronology analyses, two significant suppliers and sedimentary infilling processes are generated: (1) the Indosinian collision orogenic belt in central-northern Vietnam, Indochina has ever played significant role in Central Canyon sedimentary evolution, (2) Hainan Island once as a typical provenance restricted within eastern Central Canyon, has been enlarging its influence into the whole channel, even into the farther western regions of Qiongdongnan Basin.