An adaptive internal mode control is proposed to eliminate effectively periodic disturbance with uncertain frequency caused by input error angle of PIGA (Pendulous Integrating Gyro Accelerometer). An adaptive algorithm with periodic disturbance frequency identification on line is applied and the internal model controller parameters are adjusted to eliminate disturbance. Then the convergence of this algorithm and the stability of the system are proved by the averaging method. Simulation results verify the proposed scheme can eliminate periodic disturbance and improve the test precision for PIGA effectively.