Belonging to the field of organic-inorganic hybrid materials, the invention provides a quaternary ammonium cation and quaternary phosphonium cation-containing organic cation modified clay, its preparation method and application. The preparation method comprises: reacting a suspending solution of a sodium base treated clay mineral with quaternary ammonium cations and quaternary phosphonium cations, conducting filtering, washing, drying and crushing, thus obtaining the quaternary ammonium cation and quaternary phosphonium cation-containing organic cation modified clay with a synergistic effect. The organic cation modified clay provided in the invention has good stability, excellent weather resistance, and no toxicity. The organic cation modified clay contains quaternary ammonium cation modified clay and quaternary phosphonium cation modified clay simultaneously, and shows a synergistic antibacterial activity, so that it can be applied to plastics, rubber, fibers, coatings, adhesives, paper, wood-plastic composite materials and a variety of polymer materials to improve the antibacterial property, the flame retardance and the barrier property of polymers, and has no influence on the mechanical properties of the polymers.