INS/BDS integrated navigation data comes from different subsystems, but the hardware and software factors between different systems will lead to data synchronization between the systems, which will affect the final integrated navigation accuracy. It can be seen that data alignment is very important in the application of integrated navigation system. Aiming at this problem, a INS/BDS integrated navigation data alignment method is realized by using FPGA+DSP small navigation solution platform. The adjustable pulse excited by 1PPS of BDS receiver is used as interrupt, and the inertial sensor and satellite navigation module are captured and framed by FPGA control chip. Then the delay error is calculated and compensated by DSP, so as to achieve the synchronous alignment of INS/BDS real-time data. Experimental results show that this method can improve the position accuracy by about 50%, and can meet the requirements of data alignment, which has certain engineering application value.