A three-dimensional baroclinic shelf sea model’s numerical simulation of the South China Sea (SCS) middle and deep layer circulation structure showed that: 1. In the SCS middle and deep layer, a southward boundary current exists along the east shore of the Indo-China Peninsula all year long. A cyclonic eddy (gyre) is formed by the current in the above sea areas except in the middle layer in spring, when an anticyclonic eddy exists on the eastern side of the current. In the deep layer, a large-scale anticyclonic eddy often exists in the sea areas between the Zhongsha Islands and west shore of southern Luzon Island. 2. In the middle layer in summer and autumn, and in the deep layer in autumn and winter, there is an anticyclonic eddy (gyre) in the northeastern SCS, while in the middle layer in winter and spring, and in the deep layer in spring and summer, there is a cyclonic one. 3. In the middle layer, there is a weak northeastward current in the Nansha Trough in spring and summer, while in autumn and winter it evolves into an anticyclonic eddy (gyre), which then spreads westward to the whole western Nansha Islands sea areas. A three-dimensional baroclinic shelf sea model’s numerical simulation of the South China Sea (SCS) middle and deep layer circulation pattern that that: 1. In the SCS middle and deep layer, a southward boundary current exists along the east shore of the Indo- China peninsula all year long. A cyclonic eddy (gyre) is formed by the current in the above sea areas except in the middle layer in spring, when an anticyclonic eddy exists on the eastern side of the current. In the deep layer, a large -scale anticyclonic eddy often exists in the sea areas between the Zhongsha Islands and west shore of southern Luzon Island. 2. In the middle layer in summer and autumn, and in the deep layer in autumn and winter, there is an anticyclonic eddy ) in the northeastern SCS, while in the middle layer in winter and spring, and in the deep layer in spring and summer, there is a cyclonic one. 3. In the middle layer, there is a weak northeastward current in the Nansha Trough in spring and summer, while in autumn and winter it evolves into an anticyclonic eddy (gyre), which then spreads westward to the whole western Nansha Islands sea areas.