Metabonomics researches of Scutellariae Radix interfering pyretic pulmonary syndrome had been done, to determine the specific biomarkers of pyretic pulmonary syndrome, and to approach the mechanism that Scutellariae Radix interfered the variation of these biomarkers.Metabonomics technique, UPLC-Q-TOF/MS analytical means and PCA statistical methods were utilized to investigate the trajectory change and inter-relationship of urinary metabolome of rats treated differently.Six specific biomarkers were determined which could represent Streptococcus pneumoniae-induced pyretic pulmonary syndrome in rats. Scutellariae Radix could significantly adjust the ascended biomarkers to the normal level. Meanwhile two of these biomarkers were identified as Delta-12-prostaglandin J2 and indoxyl sulfate.There was a good therapeutic function of Scutellariae Radix on pyretic pulmonary syndrome, which was elucidated on the metabolic aspects. There was also a correlationship between the mechanism of Scutellariae Radix curing pyretic pulmonary syndrome and the six specific biomarkers.