China Customs is one of the public agencies to implement the strategy of “One Belt and One Road”. The promotion of the strategy will result in a lot of challenges for the international cooperation of China Customs. How to deal with these challenges will deeply affect customs cooperation in terms of content, focus and mechanisms. It is essential for China Customs to think about how the “One Belt and One Road” strategy will conduct the cooperation to maintain its function and to realize its strategic goal. We need to pay more attention to the “One Belt and One Road” strategy with the characteristics of neo-functionalism. This paper will use the theories of neo-functionalism to illuminate what concrete measures China Customs have taken or will take to implement the "One Belt and One Road" strategy and how to cope with the risks in the process of strategy implementation.