Background and Objective: Vegetation that is commonly used in urban design has a significant impact on air quality in the urban canyons. Thus, planners should be aware of vegetation impacts. In Isfahan metropolis, though vegetation covers a considerable portion of the city, the streets are encountered with pollution problems. In this study, distribution of pollution in urban canyons is evaluated using an optimal model for pollution reduction. Method: A three-dimensional modeling software called ENVI-met along with local and sub-climatic air quality model based on CFD-computational fluid dynamics-is used to study the influence of vegetation on pollution level in urban canyons. In this study, first a sample of real field and next a simpler version of the selected area are simulated. Findings: Different parameters such as height to width ratio in urban canyons, density of trees, location of trees in the streets and gaps between the trees are evaluated. Conclusion: The obtained results show that the increase of wind velocity in the shallow valleys is at the the lower level and the absence of natural obstacles such as trees reduces the level of pollution due to the high velocity of wind at this condition. When trees are located in the center of urban canyons, pollution and tree distances are inversely correlated and pollution level reduces by increasing the distance between the trees. In the other words, the pollution that is caught by the tree canopies decreases with the reduction in tree canopies.