The invention relates to an automatic control system for an export customs transfer, sequentially comprising a business contact table, a central processing table, a customs transfer contactor, a warehouse management system and a customs barrier receiver, wherein the input end of the central processing table is connected with the business contact table, and the output end of the same is connected with the customs transfer contactor; the other end of the customs transfer contactor is connected with the warehouse management system, and the other end of the warehouse management system is connected with the customs barrier receiver; the central processing table internally comprises a central processing module and a central execution module, wherein the input end of the central processing module is connected with the business contact table, and the output end of the same is connected with a first-level execution system; the other end of the first-level execution system is connected with theinput end of the central execution module, and the output end of the central execution module is connected with the customs transfer contactor; and a second-level execution system and a transfer table are connected between the central execution module and the warehouse management system. The invention not only has higher export customs transfer efficiency and accelerates the export customs transfer, but also has lower error rate and saves the customs transfer cost.