Abstract: Clay minerals and detrital minerals in clay fraction can be transported long distance due to small sizes, making them good indicators for multi-provenance tracing in the muddy areas of the Changjiang (Yangtze) River estuary and its adjacent areas. Based on an improved clay mineral XRD pretreatment method, the main clay mineral species and detrital minerals in clay fraction were specified. The distributions of clay minerals and non-clay minerals in the areas, and the sources and sinks of sediment in the Changjiang River estuary and the inner continental shelf were explored. The results show that the types of clay minerals in the surface sediments in the Changjiang River estuary and inner continental shelf included illite (containing 2M1 and 2M2), kaolinite, nacrite, clinochlore, and cronstedtite, whereas non-clay minerals in clay fraction included mainly quartz, potassium feldspar, plagioclase, dolomite, iron dolomite, calcite, and anhydrite. Based on the spatial distribution differences of clay minerals and non-clay minerals, the study areas could be divided into two provenance areas: the first is the northern area covering the Changjiang River estuary and the northern part of the inner continental shelf; and the second is the southern area covering the southern part of the inner continental shelf. Provenances in the former area are dominated by Changjiang River originated materials, with a few from the abandoned Huanghe (Yellow) River delta; while the latter are also dominated by Changjiang River originated materials, but with a certain amount of material from regional small-medium–sized rivers in Zhejiang and Fujian provinces. These results reveal that sediments from the abandoned Huanghe River delta in the northern Jiangsu coastal zone could transport cross the Changjiang River estuary and reach the northern part of the inner continental shelf.