A method for controlling an antenna of a mobile communication application system based on double quaternions in MEMS inertial navigation. The method comprises: introducing an antenna control quaternion based on a navigation attitude quaternion; in each interrupt cycle of a navigation computer, updating the two quaternions respectively using a carrier system measured by a gyroscope relative to a rotation vector of an ideal platform coordinate system; in each filter cycle, correcting the error of the navigation attitude quaternion respectively using a Kalman filter; according to the relationship between the attitudes determined by the two attitude quaternions, determining the angular speed in an antenna control instruction; and finally, driving a servo system to rotate at an antenna servo control angle converted by an antenna control quaternion attitude.