The disclosure provides a method and a system for automatically discovering an inference rule, a medical knowledge database and a retrieval method. The method includes: acquiring a relation matrix for each medical relation, the relation matrix representing a relationship between vectors of the medical entities having the medical relation; and acquiring the inference rules based on the relation matrices for the plurality of medical relations, each inference rule including a first medical relation, a second medical relation and a third medical relation, the inference rule representing that the third medical relation is inferred from the first medical relation and the second medical relation.