Samples to be scanned are gradually showing diversified development trends. In order to further improve the accuracy of fluorescence signal acquisition, an infrared fluorescence scanning system is designed with embedded technology as the basic environment. Using power supply circuit, LED lamp control circuit, motor control circuit, AD conversion circuit, network module, USB module, serial port module and other peripheral module circuits, the circuit architecture of the backplane is built. S3C2440 ARM processor is selected as the system processor. Through a series of processes such as three-axis stepping motor drive, current-voltage signal conversion, signal amplification and signal noise removal, the signal acquisition circuit module is improved. Based on the infrared fluorescence scanning requirements, the scanning system software functions are composed of system self-checking, paper strip detection, record search, system setting and other modules. Ring buffer queues are constructed at the upper and lower computers of the scanning system to realize the parallel operation of each module. After setting the scanning system parameters, the performance of AD conversion circuit, signal amplification circuit and double ring buffer queue of the system are evaluated. According to the experimental results, it can be seen that the system has certain validity and feasibility, and the system accuracy and transmission rate are relatively ideal.