Developing simple, rapid, and environmentally friendly synthetic methodologies for the preparation of functional nanomaterials is of great importance for broadening and improving their potential applications. In comparison with other methods, the microwave-assisted hydrothermal method possesses and combines the merits of microwave and hydrothermal methods, which can achieve the high temperature and high pressure for a short time from several minutes to several hours in a closed reaction system. In this review, the synthesis of various types of functional nanomaterials such as metals oxides, metal composite oxides, inorganic biomaterials (hydroxyapatite and calcium carbonate), and metal sulfides via the microwave-assisted hydrothermal method is summarized. The special properties and applications of functional nanomaterials by the microwave-assisted hydrothermal method are compared with others methods. The future developments of this promising method are put forward.