The basement of the South China Sea (SCS) and adjacent areas can be divided into six divisions (regions) – Paleozoic Erathem graben-faulted basement division in Beibu Gulf, Paleozoic Erathem strike-slip pull-apart in Yinggehai waters, Paleozoic Erathem faulted-depression in eastern Hainan, Paleozoic Erathem rifted in northern Xisha (Paracel), Paleozoic Erathem strike-slip extending in southern Xisha, and Paleozoic-Mesozoic Erathem extending in Nansha Islands (Spratly) waters. The Pre-Cenozoic basement in the SCS and Yunkai continental area are coeval within the Tethyan tectonic domain in the Pre-Cenozoic Period. They are formed on the background of the Paleo-Tethyan tectonic domain, and are important components of the Eastern Tethyan multi-island-ocean system. Three branches of the Eastern Paleo-Tethys tectonic domain, North Yunkai, North Hainan, and South Hainan sea basins, have evolved into the North Yunkai, North Hainan, and South Hainan suture zones, respectively. This shows a distinctive feature of localization for the Pre-Cenozoic basement. The Qiongnan (i.e. South Hainan) Suture Zone on the northern margin of the South China Sea can be considered the vestige of the principal ocean basin of Paleo-Tethys, and connected with the suture zone of the Longmucuo-Shuanghu belt–Bitu belt –Changning-Menglian-Bentong-Raub belt, the south extension of Bitu-Changning-Menglian–Ching Mai belt–Chanthaburi-Raub-Bentong belt on the west of South China Sea, and with the Lianhua-Taidong suture zone (a fault along the east side of Longitudinal Valley in Taiwan)–Hida LP/HT (low pressure-high temperature) metamorphic belt–Hida-marginal HP/LT metamorphic belt in southwestern Honshu of Japan, on the east of the South China Sea. The Qiongbei (North Hainan) suture zone may eastwards extended along the Wangwu-Wenjiao fault zone, and connects with the Lufeng-Dapu-Zhenghe-Shangyu (Lianhuashan) deep fault zone through the Pearl River Mouth Basin. The Meso-Tethys developed on the south of the South China Sea. The Nansha Trough may be considered the vestige of the northern shelf of the Meso-Tethys. The oceanic crust of the Meso-Tethys has southwards subducted along the subduction-collision-thrust southern margin of the Nansha Trough with a subduction-pole opposite to those of the Yarlung Zangbo-Mytkyina-Bago zone on the west of the South China Sea, and the Meso-Tethyan (e.g. Northern Chichibu Ocean of the Meso-Tethys) suture zone “Butsozo tectonic line” in the outer belt of the Jurassic-Early Cretaceous terrene group in southwest Japan, on the east of the South China Sea.