The paper contains research of trade flows in the Russian Federation by using of imitation model, built in AnyLogic system. The results of the research show the shortage of warehousing storage areas in several cities, and the overall lack of custom terminals. The optimization of the Russian logistics requires 2-5 times increase increase storage areas in cities experiencing logistic problems. Construction of 40% additional custom terminals can reduce the excessive distance of imported goods by 100 kilometers. Almost all derived results coincide with estimations of professional specialists in Russian logistics.