Objective To analyze the composition principles of Chinese patent drugs containing Lonicerae Japonicae Flos (Jinyinhua) in National Standard for Chinese Patent Drugs (NSCPD) enacted by Ministry of Public Health of China by using Traditional Chinese Medicine Inheritance Support System (TCMISS), and provide reference for its clinical application and development. Methods Based on TCMISS (V2.0), with methods of association rules and improved mutual information method, we analyzed the composition patterns and rules of single drugs and drug combinations. Results Through analyzing on the 201 patent drugs, 21 core drug combinations and 19 diseases that Jinyinhua commonly used were mined, from which influenza, and sore and ulcer were chosen to further analysis, including core drugs and drug combination rules, syndrome etc, disclosing the composition principles of Jinyinhua used in different diseases. Conclusion Patent drugs containing Jinyinhua collected from NSCPD mainly could clear heat and remove toxicity, and the composition principles reflect the compitable characteristics of Jinyinhua in treating different diseases, which are in accordence with clinical application of multiple-efficacy drugs.