The invention relates to the technical field of plastic assistants, and concretely relates to a novel fluorine-containing siloxane fire retardant, and a preparation method and an application thereof. The preparation method comprises the following steps: 1, uniformly mixing organosiloxane monomers, adding the obtained monomer mixture into a catalyst and emulsifier dissolved aqueous solution, and carrying out a reaction to obtain an organopolysiloxane emulsion; 2, adjusting the pH value of the organopolysiloxane emulsion by using an alkali liquid, adding a fluorine-containing styrene monomer and a copolymerization, adding an initiator, a crosslinking agent and a chain transfer agent, and carrying out a reaction to obtain an organosiloxane grafted fluorine-containing styrene polymer emulsion; and 3, diluting the polymer emulsion, adding a de-emulsifier to carry out demulsification, centrifuging the de-emulsified emulsion, and carrying out drying and crushing to prepare the novel fluorine-containing siloxane fire retardant. The novel fluorine-containing siloxane fire retardant prepared in the invention has excellent anti-dripping effect and fire-retardant property without affecting the mechanical properties of a high-molecular material polymer, and also can improve the mechanical properties and the heat resistance of matrix resin.