Over the continental shelf in the northern South China Sea (NSCS), the shelf circulation is controlled by monsoonal wind forcing, buoyancy flux from Pearl River, bottom topography and external forcing. Based on the dynamic characteristics in response to local/remote forcing, circulation over the NSCS can be uniquely divided into 4 zones. They are east of Hainan Island (EHI) with steep shelf (Zone 1), quasi-two-dimensional flow regime (Zone 2) between the Pearl River Estuary (PRE) and EHI, freshwater-influenced shelf off the PRE (Zone 3) and a narrowed-widened shelf in the eastern NSCS (Zone 4). These four zones are linked by the shelf circulation and associated dynamics processes, and they interact each other to jointly shape the spatiotemporal variations of the circulations over the entire NSCS. Based on a three-dimensional model, we investigate the unique circulation in each of these zones as well as their dynamic linkage arising from the time-dependent, three-dimensional along- and cross-shelf circulation over the shelf. Seasonally, the dense water confines typically in a closer inshore region in Zone 1 and 4 as compared with other two zones in summer, and the water is distinctly vertically uniform over the shelf in winter except in Zone 1 where downslope water transport occurs in subsurface layer. We found that the alongshore transport connects the adjacent zones, which is commensurate with the local cross-isobath transport, to characterize circulation in each zone. It is shown that the upwelling structures in Zones 2 and 3 during summer are largely modulated by upstream transport because of the relatively weak upwelling intensity and the strong alongshore transports over quasi-two-dimensional shelf topography. In contrast, the respective steep and widened shelf locally forces strong upwellings in Zones 1 and 4. During winter, the conditions are depth-independent and horizontally-uniform, because the strong along-shelf transport exceeds the local cross-shelf transport, and there is stronger mixing. The exception occurs in Zone 1 where the downstream alongshore transport is blocked by Hainan Island and a downwelling cross-shelf circulation is prominent. There is a weaker spatial variation of shelf circulation in winter than in summer when the spatially distinct upwelling structure appears along the shelf. The synoptic atmospheric variations have great impacts on the modulation of shelf circulations, which onset and offset upwelling/downwelling favorable winds and cause the disconnections in both along- and cross-shelf circulation and thus in the linkage of the zones. The relatively shorter alongshore dynamical correlation scale in Zone 4 is due to the strong variation of the cross-isobath transport modified by the topography.