The invention relates to a microorganism and enzyme mixed preparation for stripping dirt of aquatic plants as well as a preparation method and application thereof. The microorganism and enzyme mixed preparation comprises citric acid, starch, carboxymethyl chitosan, bacillus subtilis, cellulase, cysteine and diatomite. The preparation method of the stripping agent comprises the following steps of: 1, sequentially adding the substances according to the proportion; 2, uniformly stirring for 15 minutes by using a V-shaped stirrer or a three-V stirrer; and 3, mixing the obtained mixture with pond water according to a mass ratio of 1: 100 to 1: 200, and uniformly stirring to obtain the microorganism and enzyme mixed preparation for stripping dirt of aquatic plants. Dirt on the surfaces of aquatic plants is rapidly removed, and photosynthesis is improved. A high-quality ecological environment rich in aquatic plants, which is clear in water, high in dissolved oxygen content in water and few in harmful substances in the water, is provided for cultured objects.