The high purity of clay minerals is a key factor to reconstruct the palaeoclimate in clay mineralogy, however, the existence of iron minerals (such as goethite and hematite) and organics lead to the intergrowth of clay minerals and other minerals, producing other mineral impurities in enriched clay minerals. Although the removal of organics in soil sediments has been fully investigated, the occurrence state of iron minerals remains controversial, hindering the preparation of high-purity clay minerals. Therefore, the occurrence relationship of iron minerals and clay minerals in Jiujiang net-like red soils of the middle to lower reaches of the Yangtze River was investigated using the sequential separation method, which provided some implications for the removal of iron minerals in soil sediments. The results indicated that goethite and hematite were mostly absorbed on the surface of hydroxy-interlayered smectite and illite in the form of films, and the rest were absorbed by kaolinite.