Abstract： In Shennong Bencao Jing， the functions of Scutellariae Radix， Coptidis Rhizoma and Phellodendri Chinensis Cortex are similar，but their clinical use is different. Based on the main syndromes that can be treated by Scutellariae Radix，Coptidis Rhizoma and Phellodendri Chinensis Cortex recorded in Shennong Bencao Jing and Mingyi Bielu，and by referring to ZHANG Zhongjing's Shanghan Lun and Jingui Yaolve， and Beiji Qianjin Yaofang and Waitai Miyao Fang in Tang dynasty， the prescriptions containing Scutellariae Radix， Coptidis Rhizoma and Phellodendri Chinensis Cortex were analyzed in this paper to explore their difference of medical use. Scutellariae Radix， Coptidis Rhizoma and Phellodendri Chinensis Cortex can treat the binding heat of the stomach and intestines；Scutellariae Radix mainly eliminates chest vexation and treats fever；Coptidis Rhizoma mainly stops diarrhea and dysentery and eliminates epigastric masses； Phellodendri Chinensis Cortex mainly treats jaundice， sores and ulcers. The analysis of the medical use of Scutellariae Radix， Coptidis Rhizoma and Phellodendri Chinensis Cortex can provide a reference for clinical practice and for the methodology of using prescription to test medicine and exploring the medical use.