This research investigated the effects of reconstitution pH value and temperature, storage duration, sunlight exposure and reheating on the contents of vitamin B1 and vitamin D in six different kinds of formula foods for special medical purposes sold on the market. The results showed that the vitamin B1 content decreased with increasing reconstitution pH value and temperature and storage time, but was little affected by reheating. The vitamin D content decreased with storage time in sunlight. pH value and reheating had little effect on the content of vitamin D. The optimum conditions for ensuring the highest utilization ratio of vitamin B1 and vitamin D in formula foods for special medical purposes were reconstitution in acidic water (pH < 7) at 40–60 ℃, storage in darkness and preferably use immediately after reconstitution.