The imaging flash lidar has been considered as a promising sensor for the future space missions such as autonomous safe landing, spacecraft rendezvous and docking due to its ability to provide a full 3D scene with a single or multiple laser pulses. The linear-mode flash lidar has been developed and demonstrated for an autonomous safe landing on the Moon in order to provide an accurate distance measurement to the landing site and its 3D image. Yet, the Geiger-mode flash lidar has also been recognized as an emerging technology for the space missions because it is highly sensitive even to a single photon and provides the very accurate timing of photon arrival. In this study, the performance of the Geiger-mode flash lidar is simulated in the approach phase and evaluated for the autonomous landing on the Moon. Furthermore, a new statistical signal processing algorithm is proposed to remove the noise counts in order to obtain the 3D image from a sequence of laser pulses in the situation of the fast moving spacecraft. The algorithm is shown to be effective for the autonomous landing due to its ability to remove noise events under the condition of low signal-to-noise ratio and improve ranging accuracy.