Abstract: Major algal biomarkers brassicasterol, dinosterol, and long-chain alkenones, representing diatoms, dinoflagellates, and haptophytes, respectively, were analyzed in seasonal suspended particles and surface sediments near Hangzhou Bay in the inland shelf of the East China Sea. The distribution characteristics and controlling factors of algal biomarkers in particles and sediments were studied. Results show that the spatial distribution characteristics of algal biomarkers in the surface sediments of the East China Sea inland shelf are obvious, and the abundances of algal biomarkers increase with the increase of water depth. The seasonal variation of algal biomarkers in particles is prominent, and the highest abundance in summer samples. Consistent with the results of previous studies, the temporal and spatial changes of biomarkers are mainly controlled by the changes of algae productivity. Due to the abundance of nutrients, high primary productivity is mainly distributed in the waters where the dilute water away from estuaries meets offshore currents. In summer, the coastal phytoplankton productivity is the highest due to the increased influence of nutrients carried by the diluted water of the Yangtze River. In addition, our results show a significant difference between the dominant sterols in surface sediments and particles. Brassicasterols dominate in particles, while dinosterols dominate in surface sediments. In addition to the common knowledge that the organic matter in particles mainly reflects the transient nature of local sites and in the surface sediment reflects the multi-year average of a wider area, we believed that the possible late hydrogenation of brassicasterol in sediments has a significant effect, leading to a significant decrease in brassicasterol abundances relative to dinosterol in the sediments. This study emphasized the complexity of sedimentary history of biomarkers in sediments. It is important to understand the relative changes of biomarkers in surface sediments for accurate interpretation of biomarkers in sedimentary records.