The Apriori algorithm of association rules requires multiple scans of the transaction database to obtain frequent item sets, which results in the generation of a large number of candidate sets and affects the operation efficiency of the algorithm. In this paper, improved Apriori algorithm based on matrix multiplication is applied to the study of the interaction among children's anti-infective drugs, antipyretic-analgesic and anti-inflammatory drugs, and drugs for digestive system, so as to explore the rule of the combination of three kinds of drugs, and provide theoretical guidance and reference for children's clinical rational drug use.