Based on time stamp alignment and fault diagnosis technology,this paper designs an integrated navigation system to meet the actual requirements of the quad-rotor aircraft when executing tasks.The system is equipped with MEMS accelerometer and gyroscope,MEMS barometer and GPS sensor.First,a predictor is designed to align the time stamp of the GPS data,so as to synchronize the GPS data with the Inertial Navigation System (INS) data.Second,the measured data (from GPS and barometer) and the INS data are used for fault diagnosis,so as to prevent the jump of the measured data and the continuous increasing of the error of INS data.Finally,an extended Kalman filter based on time stamp alignment and fault diagnosis is used to design the integrated navigation system,so as to estimate the position and velocity of the quad-rotor aircraft.