Based on the software of Traditional Chinese Medicine Inheritance Support System (TCMISS), the article made analysis on the composition rules of prescriptions dealing with syndrome of deficiency of both qi and blood from National Standard for Chinese Patent Drugs (NSCPD) enacted by Ministry of Public Health of China. First, prescriptions were collected from NSCPD. Second, used integrated data mining methods in TCMISS, including association rules, improved mutual information method, et al. to analyze the medication rules. At last, irregular menstruation, insomnia, consumptive diseases with the same syndrome of deficiency of both qi and blood, were chosen to make comparative analysis on frequency of medicines used, core drug combinations, et al. to better find the similarities and differences of medications rules when confronted with the same syndrome while different diseases. And the similar core drug combinations directly reflected the characters of clinical practices of traditional Chinese medicine, which emphasizes on the treatment based on the syndromes of differentiation, and treating different diseases with the same methods.