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To improve the time accuracy of Linux system,a Beidou timing card driver under PCI-Express interface is designed. Timing card transmits time and location information to the FPGA (Field-Programmable Gate Array) by Beidou satellite navigation receiver module. FPGA decodes time and location information by using state machine,and creates a virtual double port RAM to store data by using IP core. When the PCI-E driver chip receives a command to read the current time,time data will be read from virtual dual-port RAM and transmit to PCI-E bus for the host computer. It programs timing card drivers for Linux including the driver compilation and loading,uses GTK+ graphical interface development tools to programming test software. Opening software and sending command to enable PCI-E driver chip hardware interrupt,when an interrupt signal output from the FPGA is found,the software runs interrupt service process will be tested and the time information on the PCI-E bus will be read and displayed in the column. Test results show that:software is stable and the interface is simple,and the timing error is 100 ns under Ubuntu Kylin system platform.