Based on the GPS technology and the embedded system, a multifunctional agricultural aircraft navigation system was designed. It combined the functions of automatic depiction of the farm outline, automatic trace planning, farm area calculation, real time trace-display and voice prompts. System hardware platform and QT environment were introduced, and the system function algorithm was discussed. The least square method was used to predict the positioning data in high-speed environments, it effectively reduced the positioning delay generated by the high-speed motion. Designing functions were achieved with the navigation system in certain field.