The vertical distribution of clay minerals in the short cores B44, YSZD01, and DH8-1 collected from typical mud deposits in the North Yellow Sea, Central South Yellow Sea, and East China Sea and associated geological significances were examined based on the analysis of Pb 210 and Cs 137 dating, ratios of kaolinite/illite and smectite/chlorite, illite crystallinity, and illite chemical index. The sediments of mud deposits of the North Yellow Sea are mainly from the Yellow River (Huang He) with that of the inner East China Sea being mainly from the Yangtze River (Changjiang), while sediment sources of mud deposits of the Central South Yellow Sea mainly include the Yellow River and the old Yellow River delta. For cores B44 and DH8-1 with a single main source, both illite chemical index and illite crystallinity have a close relationship with temperature and precipitation in the sediment-source river basin except for YSZD01 with a multi-source. Generally, the ratios of kaolinite/illite and smectite/chlorite indicate that chemical weathering strengthens while physical weathering weakens within the source river basin for the mud sediments from the North Yellow Sea to the Central South Yellow Sea to the East China Sea. In general, illite percentage would decrease, while kaolinite percentage would increase for cores B44, YSZD01, and DH8-1 if the East Asian Winter Monsoon was enhanced in the past 100 years.