Eutrophication has become a major global environmental concern. As the main factor responsible for freshwater lakes and reservoirs eutrophication, the excessive input of phosphorus (P) initiates phytoplankton blooms as well as the significant reduction in dissolved oxygen and transparency in lake, thus secreting algae toxins and derived odor substances which seriously threaten the ecosystem and human life. When the external inputs are effectively curbed, the control of internal-P loading including eutrophic water and sediment directly determines the effectiveness of eutrophication. Clay minerals are a kind of nonmetallic mineral resources widely distributed in nature. It has been extensively applied in ecological environment restoration and management in recent years, ascribing to its large specific surface area, porosity and the excellent surface adsorption and ion exchange performance. This paper introduced the main types of clay minerals and their physicochemical characteristics, summarized the advantages and disadvantages of different modification methods on typical clay minerals, presented the latest research results of its application in P control of eutrophic water and sediment, discussed the factors influencing the mechanism of P removal and their potential ecological environment impact, and pointed out the future research direction.