The invention discloses an epoxy modified organic silicon resin adhesive and a preparation method thereof. The adhesive is prepared from the following components of 10-30 parts of polyurethane modified epoxy resin, 20-70 parts of epoxy modified organic silicon resin, 20-60 parts of fluorene-based epoxy resin, 10-40 parts of carboxyl-polybutadiene acrylonitrile liquid rubber, 10-60 parts of curing agent, 1-8 parts of thixotropic agent, 0.5-3 parts of compound accelerator and 2-6 parts of coupling agent. The preparation method comprises the steps of weighing each component according to the ratio, evenly mixing the polyurethane modified epoxy resin, the epoxy modified organic silicon resin, the fluorene-based epoxy resin and the carboxyl-polybutadiene acrylonitrile liquid rubber under agitation at 50-70 DEG C; adding the curing agent, the thixotropic agent and the coupling agent and heating to 70-90 DEG C; evenly agitating, and cooling to room temperature after vacuum defoaming; and adding the compound accelerator under agitation at 40-50 DEG C until evenly mixing. The modified epoxy resin adhesive is good in adhesion and simple in process, and has good adhesion on materials such as metal, glass, and plastic ceramic.