In this invention, first It is set that an object of study of a compound traditional Chinese medicine with its chemical compositions being clear about. The molecules of chemical constitutions of each ingredient of the Chinese medicine prescription are collected and reorganized, and setting a data base for chemical constitutions molecules of said Chinese medicine prescription. For the aim of pharmacodynamics effects of main therapeutical functions of the traditional Chinese medicine prescription with their clear therapeutical effects, clear mechanism and definited target spots, we search or set up the corresponding molecular target spots. Three procedures (without odor of priority) are: poisonousness sieving, analogous medicine properties estimation and molecular abutment decision to these molecular data base of the set pharmacodynamics models respectively. Finally we estimating all the molecules in the molecular data base, selecting-out the molecules with higher grading, to obtain the pharmacodynamics effect P(i) molecular pre-prescription, and then producing novel prescriptions.