Three-dimensional blended data, comprised of amplitude and coherence cubes, are used to analyze the evolution of the Central Canyon System (CCS) since the Late Miocene within the western Qiongdongnan Basin (QDNB), South China Sea. The evolution of the canyon since the late Miocene includes two phases and five stages, with a dramatic change of deepwater sediment bodies from early, predominantly axial channel-levee deposits (CLDs) to late, primarily side mass-transport deposits (MTD). During the first and second stages (approximately 5.3–3.7 Ma), axial CLDs derived from the western slope of the South China Sea dominated the sediment bodies within the canyon. The last three stages (3.7 Ma to Recent) were dominated by side MTD, which originated from the northern slope of the South China Sea. Since the canyon was completely filled at 2.4 Ma, axial CLDs only reactivated in the lower strata of the most southern region of the study area. The time of formation of the CCS (approximately 11.6–8.2 Ma) is almost synchronous with the rise of the Himalayas and the first enhancement of the East Asia monsoon during the middle and late Miocene. The change of deepwater deposits within the canyon, which has varied from CLDs to MTDs since 3.7 Ma, is in phase with the further rapid uplift of the entire Tibetan Plateau and the second enhancement of the East Asia monsoon during the middle Pliocene. This evidence suggests that the formation and filling of the canyon should be controlled by the evolution of the Tibetan Plateau and the East Asia monsoon. Tectonics and the East Asia monsoon controlled the evolution of the CCS by changing erosion rates from the Tibetan Plateau, South China Block, and Indochina Peninsula, and sedimentary rates within the Yinggehai Basin and QDNB.