A food composition containing bee embryo capable of effectively reducing allergen component and a manufacturing method thereof are provided. It is characterized in that the food composition containing low-molecular bee embryo is manufactured by using a protein-decomposing enzyme to process the bee embryo or processed materials thereof. Besides, in the result of using the gel filtration chromatography to process the manufactured low-molecular bee embryo, a peak area of macromolecule having molecular weight above 12,000 is less than one percent of total peak area. In the manufacturing method of the food composition containing the low-molecular bee embryo, it is characterized that a step of using acid protease or neutrase to process the bee embryo or the processed materials thereof is provided.
