The invention relates to a preparation method of a water repellent agent for packaging paper and a paper board and application thereof and belongs to the technical field of paint. The preparation method comprises the following steps: firstly, placing absolute ethyl alcohol, a coupling agent and fumed silica in a glass container to uniformly mix and stir according to a certain proportion; then adding a solvent and after the solvent is sufficiently mixed with the solution obtained in the step 1, carrying out high-speed homogeneous dispersion of mixed solution on a homogenizer; in the using process of the prepared water repellent agent, regulating different proportions according to the requirements of application base materials. The water repellent agent can be coated, also can be sprayed, is convenient to apply and is rapid to form a film; after the surface of a coating is dry, the coating is dried for 30min at a temperature of 120 DEG C so as to obtain a paper packaging product with the surface water repellency. The water-repellent coating has high transparence and high water repellency; the paper board has low water absorption; the coating has a good adhesion force; the base material applied with the water repellent agent is coated with the water repellent agent.