The present invention relates to a method for modeling and simulating a biochemical pathway and a system for the same, more particularly to a method for modeling and simulating a biochemical pathway which comprises: developing a mathematical dynamics model that applies biological data of a signal transduction pathway within a biological system such as protein concentration as a parameter; and simulating by using the same. The present invention enables protein functions, activation, interactions between proteins, signal transduction pathways and the like to be determined under overall environment, and a network of signal transduction to be understood in both quantitative and qualitative level. The simulation model of the present invention can be utilized to develop novel substances for a specified use such as medicine design even in a minimal trial. Further, it may promote to easily predict their application to improve the quality of target substance.