The invention discloses a Chinese herbal medicine preparation for controlling dysentery of apalone ferox and a preparation method thereof, belonging to the technical field of chelonian feed additive processing. The Chinese herbal medicine preparation is prepared from the following raw materials: orange peels, common andrographis herb, rhubarb, garlic, cassia bark, peppermint, leaves of balsam pear, baikal skullcap root, indigowoad root, Indian buead, heartleaf houttuynia herb, hyssopus officinalis, Japan clover herb, liquorice root and Chinese cinquefoil herb. The Chinese herbal medicine preparation is prepared through the steps of drying, grinding, sieving, mixing, granulating, drying, cooling, packaging, and the like. The Chinese herbal medicine preparation has the beneficial effects that the Chinese herbal medicine preparation integrates the effects of various Chinese herbal medicines and can achieve the functions of clearing heat-fire, eliminating dampness and regulating the middle warmer and removing toxicity; the apalone ferox has good preparation absorption effects, and the Chinese herbal medicine preparation takes effect quickly, has long duration and can achieve the effects of enhancing the disease resistance of the apalone ferox, effectively controlling dysentery of the apalone ferox, increasing the survival rate of the apalone ferox and reducing the risks of farmers; the Chinese herbal medicine preparation is simple in preparation method and low in production cost and is beneficial to popularization and application.