To civil aircrafts, safety is the most important.The Flight Management System (FMS) is an airborne equipment essential to guarantee the flight safety of the civil aircraft.Under the deception jamming to GPS, the safety of the FMS navigation determines whether the aircraft can fly safely in the designated airspace or not.Taking a certain foreign FMS as the object for test, we established a test platform and made experiments to study the effect of GPS deception jamming signals on FMS navigation safety.The study supplies a basis and technical support for improving the safety level in FMS development.