According to the model of multipath propagation in low-angle tracking, the reflecting surface height has significant influence on the measurement precision of the target height. In this study, a novel method for the joint estimation of the target height and the reflecting surface height is proposed based on multichannel digital array radar. To reduce the computational burden of the proposed method, the projection gradient method instead of two-dimensional search is adopted to minimise the cost function. Moreover, the Cramer–Rao bound of the proposed method is also derived in this study. At last, simulations and practical data processing results show that the proposed method has a good estimation precision.