Photon counting LiDAR can capture the 3D information of long-distance targets and has the advantages of high sensitivity and high resolution. However, the noise counts restrict improvements in the photon counting imaging quality. Therefore, how to make full use of the limited signal counts under noise interference to achieve efficient 3D imaging is one of the main problems in current research. To address this problem, in this paper, we proposes a 3D imaging method for undulating terrain depth estimation that combines constant false alarm probability detection with the Bayesian model. First, the new 3D cube data are constructed by adaptive threshold segmentation of the reconstructed histogram. Secondly, the signal photons are extracted in the Bayesian model, and depth estimation is realized from coarse to fine by the sliding-window method. The robustness of the method under intense noise is proven by sufficient undulating terrain simulations and outdoor imaging experiments. These results show that the proposed method is superior to typical existing methods.