The sedimentary rhythm is well developed in the environment which is controlled by strong seasonal climate changing condition. This rhythm is important for sediment core dating purpose. In this study, we examine muddy sediments on the inner continental shelf of the East China Sea that are influenced under seasonal change of the East Asian monsoon. We use Ensemble Empirical Mode Decomposition (EEMD) method to process sediment grain size and X-radiograph negatives grayscale value data in three sediment cores from this area and use the results to analyze the patterns of sedimentary variability and the causes of cyclic variability of the sedimentary process. The variability in the grain size and grayscale values of the core sediments has three components: the high-frequency variability, low-frequency variability and a secular trend. Among these components, the high-frequency component reflects variability on annual time scale can be well recognized, we suggest that the annual variability is derived from seasonal variation in the sediment flux from the Yangtze River to the sea, as well as the East Asian monsoon's impact on the sedimentary dynamics of the East China Sea's inner continental shelf. However, the other variability is hard to identify which cycles there are. This variability may reflect decadal winter monsoon oscillation and human activity of dam construction in the Yangtze River. Each annual variability presents a varve in the sediment sequence, which can be used to determine the sediment deposition rate and accurately date the core sediment. We found that the average deposition rates of the three cores from north to south on the inner shelf were 3.1 cm/yr, 1.0 cm/yr, 0.9 cm/yr, indicating that the Yangtze-derived sediment decreased with the increasing distance from the Yangtze estuary to the shelf. The deposition rate of each core varies over time, and the maximum deposition rate can be 3–5 times greater than the minimum rate. The sediment ages obtained from varve chronology and radiometric dating are fairly consistent on a centennial scale, differing only by 2–5 years. Thus, varve counting is a useful supplementary approach to radiometric age dating for constructing chronologies for core sediment in shelf seas influenced by monsoons.