The invention discloses a missile interference identification algorithm, which belongs to the field of missile flight test data analysis, and comprises the following steps: 1, preprocessing angular velocity information acquired by an inertial measurement device, including unit transformation and high-frequency noise filtering; 2, selecting a proper time interval according to the processed angularvelocity information, and resolving angular acceleration information; 3, according to the angular acceleration information and the moment of inertia of the missile, solving the total moment componentof each axis under the missile system; 4, according to the Mach number, the synthetic attack angle, the airflow roll angle, the mass center, the rudder deflection angle and other information, solvingtorque components of all shafts under a missile system under the free flow of the missile; and 5, subtracting the moment flowing down freely from the total moment of each shaft under the projectile system to obtain a projectile disturbance moment component of each shaft under the projectile system. According to the missile interference identification algorithm, high-frequency signals are filteredout in a targeted mode, and phase lag is reduced as much as possible, and it is ensured that the processed angular velocity information can be used for extracting mechanical missile interference.