Railway clearance detection system based on rotating laser scanner sensors was designed for the realization of non-contact detection of railway clearance. In the system, in order to acquire and synchronize the data of Laser scanner sensors, gyroscope, position transducers and speed sensor, the FPGA-based PCI data acquisition synchronization card was designed. This paper describes the hardware design for acquisition synchronous card, PCI interface chip configuration, FPGA core programming. The experiment proved that using the data acquisition synchronization card, 2-channels of 500k baud rate serial data, 1-channel of 115200 baud serial data, 4-channel A/D, 2-channel high-speed IO signals can be acquired and synchronized, the time accuracy is 1ms, without missing data. This ensures reliable operation of the whole railway clearance detection system.