The relevance of this study is due to the fact that the innovation customs technologies adoption can accelerate and simplify the customs operations, improve the efficiency of the customs control and ensure the organization of the «single window» and e-customs functioning. The article deals with the innovation customs technologies that are used by the customs authorities of the Russian Federation and the participants of the foreign economic activity. In this paper the authors propose new targets that evaluate the activity of the customs officers that address the customs operations, as well as their formulas. The main problems of customs technologies application are revealed and the recommendations for improving the innovation customs technologies adoption are given.