Investigating the spatiotemporal variability of biogeochemical processes and ecological responses under multiple physical controls in shelf seas is of great importance for obtaining an in-depth understanding of marine ecosystem. Based on a compiled data set of historical observations and remote sensing data, the spatiotemporal variability and heterogeneity of physical-biogeochemical processes in the semi-enclosed South Yellow Sea (SYS) are investigated, and the intrinsic connectivity among different subregions and the associated mechanisms are examined. The results show that the seasonal alternation between southward transport in cold seasons and upwelling-induced vertical delivery in warm seasons is the primary physical control of the biogeochemical processes and primary production off Shidao and in the area adjacent to the Haizhou Bay. The northeastward expansion of coastal waters in the Subei Shoal constitutes an important physical driver for the offshore transport of Ulva prolifera in summer. Stratification significantly affects the biogeochemical processes in the Yellow Sea Cold Water Mass (YSCWM)-dominated area during warm seasons, and nutrients can accumulate in bottom waters from spring to autumn, making the Yellow Sea Cold Water Mass (YSCWM) be an important nutrient pool. Upwelling around the YSCWM boundary in the stratified season leads to consistency among the high chlorophyll a (Chl a) area, high primary productivity region and low-temperature upwelling zone. During cold seasons, the interactions of the southward cold waters in the western nearshore area and the northward warm waters in the central region lead to an “S”-shaped front in the SYS. In summer, upwelling can extract nutrients from the YSCWM; thus, the biogeochemical-ecological processes inside the cold-water mass and in the frontal zone are well connected via upwelling, and three typical physical-biogeochemical coupling regions are generated, namely, the Shidao coast, the area beyond the Haizhou Bay and the area off the Subei Shoal. This work refines and integrates studies on regional oceanography in the SYS and provides a comprehensive and systematic framework of physical-biogeochemical-ecological processes.