The Position and Orientation measurement System (POS) is a dedicated Strapdown Inertial Navigation System (SINS)/Global Positioning System (GPS) integrated system for airborne remote sensing. In-flight alignment (IFA) is an effective way to improve the accuracy and speed of initial alignment for an airborne POS. During IFA, the GPS provides the position and velocity references for the SINS, so the alignment accuracy will be degraded by unstable GPS measurements. To improve the alignment accuracy under unstable GPS measurement, an adaptive filtering algorithm of an extended Kalman filter (EKF) combined with innovation-based adaptive estimation is proposed, which introduces the calculated innovation covariance into the computation of the filter gain matrix directly. Then, this innovation adaptive EKF algorithm is used for the IFA of the POS with a large initial heading error. Moreover, it is optimized by blocked matrix multiplication to reduce the computational burden and improve the real-time performance. To validate the proposed algorithm, the car-mounted IFA experiment is carried out for the prototype of the airborne POS (TX-D10) under a turning maneuver, taking Applanix's POS/AV510 as a reference and changing the GPS measurement artificially. The experiment results demonstrate that the proposed algorithm can reach a better alignment accuracy than the EKF under unknown GPS measurement noises. [ABSTRACT FROM PUBLISHER]