The combinational navigation computer system on the chip is designed by using Virtex-4 FPGA. Using FPGA embedded PowerPC hard core processor, this navigation computer carrys out the navigation operation. Using the integral IP core in the FPGA logic, the control, the bardware acceleration of the interface communication and the part operation are realized. The integral degree of the system is enhanced. Furthermore, this system can be re-configurated. And then on different situations it makes the navigation system meets the requirement for the interface and function.