The study of critical geological processes of sediments from source to sink in the East China Sea (ECS) is of great significance for further understanding the surface processes, material cycling, and sedimentary evolution in the East Asian continental margin. Based on the high-resolution clay mineralogy and REEs in fine-grained sediments of Core CSHC-15, this study has analyzed the periodic transition mechanism of sinks in fine-grained sediments in the ECS from a source-to-sink perspective. The clay mineral provenances of Core CSHC-15 exhibited distinct periodic abrupt shifts between the Changjiang and Taiwan island over the past 200 kyr, indicating the periodic transitions of sinks in fine-grained sediments between the inner shelf of the ECS and the Okinawa Trough. When the sea level rose or fell to a critical depth (around −25 m or −50 m), the changes in the accommodation space of the continental shelf and the shelf fronts were the direct factors leading to the periodic transitions of sinks in fine-grained sediments in the ECS. The intense eccentricity cycles (100-kyr) of the clay mineral parameters of Core CSHC-15 reflected the impacts of the East Asian Winter Monsoon (EAWM). This study confirms that long-term (eccentricity and longer cycles) climate signals of the source areas can be extracted from the clastic sedimentary records of the ECS. The new finding highlights the periodic transition mechanism of sedimentary sinks in the ECS that will promote the progress of sedimentary geology since the Late Quaternary.