There are several cycles of coastal line migration and water-land inversion in the northwestern South China Sea due to climate and sea level changes during late Quaternary. Seven seismic reflectors have been recognized and dated based on high resolution seismic profiles and drilling cores. The inversion of late Quaternary (100.1~40.7 kaBP) paleo-water depth and coastal line have been build based on modern water depth, global sea level change curves and thickness of sediment in the study area. The inversion results indicate that part of the coastal line in western, northwestern and southern Hainan Island migrated seawards 100.1 kaBP. The water depth was larger than 550 m with a narrow shelf in the study area then. The shelf area became larger with a flat sea floor at 78.1 kaBP. The western coastal line migrate to sea in large scale with more land area exposed.The water depth was less than 200m. Factors suggest that the paleo-water depth and coastal line was controlled by climate, sea level changes and sediment supply.