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The molecular recognition plays an important role in biological activity in nature and most biological separation techniques depends on the role of molecular recognition. The molecular imprinting technique has developed rapidly. It has been used in many fields widely, such as chromatography, simulation of antibody or receptor, simulation of biosensors and enzyme and synthesis of catalyst. Molecular imprinting technique is a method to synthesize molecularly imprinted polymer (MIP) and the molecularly imprinted polymer has the function to identification for the target molecule (it is called template molecule). Molecularly imprinted polymer has got a lots of interest because of its versatility and amazing stereospecific recognition. The study on the recognition performance of different functional monomers on the molecularly imprinted polymer has important significance for improving the affinity and selectivity of a molecularly imprinted polymer. The computational chemistry methods were introduced for the study of the synthesis of molecularly imprinted polymer recently, It can reduce the number of experimental synthesis conditions greatly and reduce unnecessary consumption of reagents and labor and it has a guiding role in improving the efficiency to research and development of molecularly imprinted polymer. The results of quantum chemical calculations have more instructive because of its higher accuracy. Cotinine is the major metabolite of nicotine. It satisfies the conditions to be an ideal biological markers, such as high Computer Simulation Study on the Effect of Recognized Characteristics of Cotinine Imprinted Polymer with Different Functional Monomers