The problem of registration for airborne multiplatform sensor based on the square root unscented kalman filter (SRUKF) in a fusion system is considered. First, a registration model for misaligned sensors was given. Then, the sensor misalignments and target states were incorporated into an augmented dynamic model, then the observability of the model was discussed and SRUKF was proposed to estimate target states and register these sensors simultaneously. The linearization of the nonlinear equation was not needed and the amount of calculation was reduced compared to UKF. Simulations demonstrate the effectiveness of the proposed algorithm. SRUKF has faster convergence speed and computational speed compared to UKF simultaneously.