This study was designed to evaluate the potential effective components of Fangji Huangqi Tang for the treatment of nephrotic syndrome based on a pharmacokinetic/pharmacodynamic model. To quantify the relationships between the pharmacokinetics and pharmacodynamics of fangchinoline and tetrandrine, the pharmacokinetic/pharmacodynamic model was set up by combining pharmacokinetic parameters and the effective indexes in rats. Compared with a model group, the effective indexes including serum urea nitrogen, cysteine protease inhibitors C, total cholesterol and triglycerides in the FHT group became significantly lower with a dosing time extension. The pharmacokinetic/pharmacodynamic modeling results showed that there were good linear relationships between the areas under the concentration-time curves and these effective indexes. Finally, fangchinoline and tetrandrine were proved to be the main effective chemical materials of FHT to cure nephrotic syndrome in rats.