As a growing number of exploration missions have successfully landed on the Moon in recent decades, ground infrastructures, such as radio beacons, have attracted a great deal of attention in the design of navigation systems. None of the available studies regarding integrating beacon measurements for pinpoint landing have considered uncertain initial beacon locations, which are quite common in practice. In this paper, we propose a radio beacon/inertial measurement unit (IMU)/altimeter localization scheme that is sufficiently robust regarding uncertain initial beacon locations. This scheme was designed based on the sparse extended information filter (SEIF) to locate the lander and update the beacon configuration at the same time. Then, an adaptive iterated sparse extended hybrid filter (AISEHF) was devised by modifying the prediction and update stage of SEIF with a hybrid-form propagation and a damping iteration algorithm, respectively. The simulation results indicated that the proposed method effectively reduced the error in the position estimations caused by uncertain beacon locations and made an effective trade-off between the estimation accuracy and the computational efficiency. Thus, this method is a potential candidate for future lunar exploration activities.