The invention discloses chocolate candies injected with probiotics and a preparation method of the chocolate candies. According to the candies, microcapsules containing bifidobacterium lactis and lactobacillus acidophilus wrap probiotic dry powder and are evenly mixed with low-sweetness massecuite, then chocolate injection is conducted, and the massecuite is prepared from freeze-dried probiotic powder, high fructose corn syrup, butter, condensed milk, fresh milk, modified starch, whole milk powder, sodium alga acid, lactic acid and salt. Chocolate injection is conducted on the prepared massecuite, and the chocolate candies injected with probiotics can be obtained. Chocolate is externally hung on the candies, the candies are of concentrated fragrance, sweet greasy, filled with the massecuite, sweet and sour and soft, the taste matching is appropriate, and to keep the probiotic activity of bacterial powder, the mixing temperature of the massecuite and the bacterial powder and the operation temperature of chocolate injection are each controlled to be within 20-50 DEG C.