Phytoplankton dynamics, which are highly sensitive to the ecosystem condition and change, are different in coastal waters and open ocean. Previous researches mainly focused on the open ocean dynamic in the South China Sea (SCS), but few research on the Eastern Guangdong (EGD), especially during a period of downwelling-favorable winds. In fact, the influence of topographic irregularities, downwelling, continental outflows, and cold, nutrient-rich currents from Fujian-Zhejiang coastal waters (ZFC) of the East China Sea (ECS) on the spatial distribution of Chlorophyll a (Chl a) in EGD coastal waters could be significant. This study utilized ocean color time series and meteorological and hydrographic data jointly from July 2002 to June 2020 to investigate the heterogeneous regional specific distribution pattern of Chl a in EGD and the environmental determinants in different regions subdivided by water depth. Then the temporal and spatial distribution pattern of Chl a in EGD in winter were discussed in detail by applying an Empirical Orthogonal Function (EOF) analysis, GaoFeng-1 (GF-1) satellite data and in situ measured dataset. The sea surface temperature (SST) in February was negatively related with Chl a in shallow coastal waters less than 60 m deep due to the nutrient-rich, cold waters from ZFC. The monthly mean photosynthetically active radiation (PAR) and precipitation showed significant effects on the phytoplankton growth over regions with a depth less than 10 m. An area with higher Chl a concentration in the downwelling zone were detected in winter. By an examining the temporal variability in meridional distribution of the mean Chl a at 22.41°N and 22.21°N, a symmetrical peak was observed. The coastal fronts extended southwestward from the southeastern coast of Guangdong Province to Dangan Island in the SCS. In addition, a cross-shelf filament was detected near the coast of Shanwei, Guangdong, China on 8 January 2020.