The invention relates to a one-component flexible polymer waterproof mortar material and a method for preparing waterproof mortar by using the one-component flexible polymer waterproof mortar material. The waterproof mortar material comprises the following powder: cement, sand, rubber powder, cellulose, fiber, silica fume, a defoaming agent, a water reducing agent, a waterproof agent and the balance of a silicon-aluminum material. According to the selected value ranges, the specific powder is selected, matched and added into a stirring device for sufficiently stirring, and a finished product of the one-component flexible polymer waterproof mortar material can be obtained after evenly mixing. The method for preparing waterproof mortar comprises the steps of burdening, adding water and mixing, and treating. The one-component flexible polymer waterproof mortar material and the method have the advantages that the flexible polymer waterproof mortar obtained after evenly mixing the waterproof mortar material and the water has the durability of mortar and certain flexibility so as to prevent cracking and water seepage, and meanwhile the flexible polymer waterproof mortar is ultra-thin, high in anti-permeability, high in wear resistance, good in anti-permeability and waterproof performance, proper in strength, and good in flexibility, impact resistance and cohesive property. The preparation method of the waterproof mortar is easy to grasp and high in efficiency, and can be used for guaranteeing the product quality.