In order to implement high precision four rotor aircraft navigation that puts forward the complementary filter method and the quaternion algorithm for sensor data amended, it can restrain the interference of the maximum error and improve the accuracy of attitude Angle calculating. First of all, a simple algorithm of strapdown inertial navigation system was deduced basic principle and use the complementary filter algorithm was improved, the inertial navigation system is given and then the mechanical layout model analysis of rotor aircraft motion. Finally simulation data selection of inertial instrument MPU6050 and HMC5883 simulation analysis was made on the measured data, platform selection STM32 processor to simulate inertial instrument measurement speed, eventually get the experimental results show feasibility of the algorithm.