In this study, deep circulation in the South China Sea (SCS) is investigated using results from mesoscale-eddy-resolving, regional simulations using the Hybrid Coordinate Ocean Model (HYCOM) verified by continuous current-meter observations. Analysis of these results provides a detailed spatial structure and temporal variability of the deep circulation in the SCS. The major features of the SCS deep circulation are a basin-scale cyclonic gyre and a concentrated deep western boundary current (DWBC). Transport of the DWBC is ~ 2 Sv at 16.5°N with a width of ~ 53 km. Flowing southwestward, the narrow DWBC becomes weaker and wider. The model results reveal the existence of 80- to 120-day oscillation in the deep northeastern circulation and the DWBC, which are also the areas with elevated eddy kinetic energy. This intraseasonal oscillation propagates northwestward with a velocity amplitude of ~ 1.0 to 1.5 cm s−1. The distribution of mixing parameters in the deep SCS plays a role in both spatial structure and volume transport of the deep circulation. Compared with the northern shelf of the SCS and the Luzon Strait, deep circulation in the SCS is more sensitive to the large vertical mixing parameters of the Zhongsha Island Chain area.