The invention relates to a Chinese herbal medicine fermentation fertilizer capable of preventing cucumber wilt disease, and a preparation method thereof. The Chinese herbal medicine fermentation fertilizer comprises the following raw materials: seaweed, enteromorpha, mikania micrantha, liquorice, black false hellebore, radix sophorae flavescentis, celeries, molasses, silica sol, an EM microbial agent and a soil modifier. The preparation method comprises the following steps: mixing and grinding the Chinese herbal medicine raw material, adding the molasses, the EM microbial agent and a proper amount of water, and conducting anaerobic fermentation at normal temperature; evenly mixing the fermentation product with the soil modifier and preparing particles; adding the mixed particles into a fluidized bed coating machine, spraying silica gel at 50-55DEG C for coating, cooling and sieving to obtain the Chinese herbal medicine fermentation fertilizer. By compounding the fermented Chinese herbal medicine with the soil modifier, and then coating to form a sustained-release fertilizer, the fertilizer not only has the functions of being synergistic, promoting plant to absorb nutrients and playing sustained-release action, but also can effectively inhibit the proliferation of cucumber wilt disease pathogenic bacteria, control the disease scale and degree, thus realizing the restoration and improvement of soil ecological environment, and avoiding environment pollution.