Objective:To analyze the composition rules of oral prescriptions in the treatment of headache,stomachache and dysmenorrhea recorded in National Standard for Chinese Patent Drugs (NSCPD) enacted by Ministry of Public Health of China and then make comparison between them to better understand pain treatment in different regions of human body.Methods:Constructed NSCPD database had been constructed in 2014.Prescriptions treating the three pain-related diseases were searched and screened from the database.Then data mining method such as association rules analysis and complex system entropy method integrated in the data mining software Traditional Chinese Medicine Inheritance Support System (TCMISS) were applied to process the data.Results:Top 25 drugs with high frequency in the treatment of each disease were selected,and 51,33 and 22 core combinations treating headache,stomachache and dysmenorrhea respectively were mined out as well.Conclusions:The composition rules of the oral prescriptions for treating headache,stomachache and dysmenorrhea recorded in NSCPD has been summarized.Although there were similarities between them,formula varied according to different locations of pain.It can serve as an evidence and reference for clinical treatment and new drug development.