An identification control method and system for a valuable document. The system comprises a collection part, an identification part, a control part, a transmission part and an upper computer. In the identification part, complete identification information about a valuable document is split into basic identification information and high-grade identification information. Only the basic identification information which is required by the control part is sent to the control part, and the information which is not required by the control part is directly sent to the upper computer by the identification part. The identification part only transmits the basic identification information to the control part, the data transmission amount is one-tenth of the original data transmission amount, and the transmission speed can be increased by 10 times, thereby solving the problem that a valuable document cannot be quickly processed continuously because the serial transmission speed between the control part and the identification part is slow.