The UnScented QUaternion Estimator (USQUE) has been approved as a promising substitute for the extended Kalman filter when applied in the Standard Inertial Navigation Equations (SINE)-based inertial navigation system/global positioning system integration. However, the expensive computational burden makes it untenable in real time applications. In this paper, a computationally efficient filtering algorithm called Marginalised USQUE (MUSQUE) is derived by embedding the Marginalised Unscented Transformation (MUT) that is applicable to nonlinear systems with a linear substructure into the widely used USQUE. The contributions of the MUSQUE developed here are twofold. Firstly, the SINE are reconstructed to be only nonlinear in the attitude quaternion while linear in velocity and position, which makes the MUT potentially applicable in the USQUE. Secondly, the quaternion and generalised Rodrigues parameter-based sigma points are propagated simultaneously in the MUSQUE to deal with the dimensional mismatching hierarchy of the USQUE. Compared with the USQUE the number of sigma points can be decreased substantially, thereby making the applied MUSQUE computationally tenable. The experimental results show that the proposed MUSQUE has nearly identical performance with the USQUE but with much reduced computational burden.