The invention relates to the technical field of aircraft simulation and particularly to a simulation system and method for simulating the autonomous flight of multiple aircrafts. The simulation system comprises a multichannel satellite signal simulator, a geomagnetic field simulator and multiple aircrafts each including a dynamics platform, a magnetic field measuring instrument, a GNSS receiver, a flight controller. The simulation system and simulation method synchronize the time of the aircrafts and respective modules by a clock module, forms a data closed loop, achieves ground simulation for simulating the autonomous flight of the multiple aircrafts, overcomes a problem that the time of the multiple aircrafts is difficult to synchronize during manual simulating aircraft simulation, and can verify the effectiveness of a multi-aircraft formation autonomous navigation and control scheme and the time synchronization of multi-aircraft time so as to evaluate the flight effect of the overall formation flight.