Acetonitrile and toluene are solvents commonly used for the synthesis of atrazine molecularly imprinted polymers (MIPs), but their effects have seldom been compared in the same imprinting system. In this paper, effects of the two solvents in an atrazine molecular imprinting system were evaluated theoretically and experimentally. A polarizable continuum model was adopted, and it was found that using the two solvents, the energy difference for the atrazine–methacrylic acid complex between vacuum and solution was not the same. The two types of MIPs prepared using different solvents vary in morphology, porosity, binding capacity, and specificity. All of these results suggest that the abilities of the solvents used to form hydrogen bonds with other compounds in the system are different. The porogen imprinting effect of the solvents also has an influence on binding capacity. Compared to MIPs synthesized using acetonitrile as solvent (MIPs‐ACN), MIPs synthesized using toluene as solvent (MIPs‐PhMe) have fewer but larger pores and exhibit much higher adsorption capability but less rigorous specificity. © 2018 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2019, 136, 47190.