Based on analyses of more than 600 surface sediment samples together with large amounts of previous sedimentologic and hydrologic data, the characteristics of modern sedimentary environments and dynamic depositional systems in the southern Yellow Sea (SYS) are expounded, and the controversial formation mechanism of muddy sediments is also discussed. The southern Yellow Sea shelf can be divided into low-energy sedimentary environment and high-energy sedimentary environment; the low-energy sedimentary environment can be further divided into cyclonic and anticyclonic ones, and the high-energy environment is subdivided into high-energy depositional and eroded environments. In the shelf low-energy environments, there developed muddy depositional system. In the central part of the southern Yellow Sea, there deposited the cold eddy sediments under the actions of a meso-scale cyclonic eddy (cold eddy), and in the southeast of the southern Yellow Sea, an anticyclonic eddy muddy depositional system (warm eddy sediment) was formed. These two types of sediments showed evident differences in grain size, sedimentation rate, sediment thickness and mineralogical characteristics. The high-energy environments were covered with sandy sediments on seabed; they appeared mainly in the west, south and northeast of the southern Yellow Sea. In the high-energy eroded environment, large amounts of sandstone gravels were distributed on seabed. In the high-energy depositional environment, the originally deposited fine materials (including clay and fine silt) were gradually re-suspended and then transported to a low-energy area to deposit again. In this paper, the sedimentation model of cyclonic and anticyclonic types of muddy sediments is established, and a systematic interpretation for the formation cause of muddy depositional systems in the southern Yellow Sea is given.