Abstract: A dynamic mathematical model of two components in preparative gas chromatography column is first advanced on the basis of studying models of the separation of analytical gas chromatography,including mass balance equations, adsorption balance equations and mass transfer equations. The simulation model of this process consists of non-linear partial differential equations. The effect of various parameters and characteristic parameters of chromatography column such as filling density, velocity of mobile phase and sample size on chromatographic separation are well analyzed by solving with numerical method.The simulated results are in good agreement with the literature data and the maximum deviation is less than 4.86%. So the model supplies certain guidance for the scale of the practical application and the optimization of the process control and operation parameters of preparative gas chromatography.