The retrieval of tree height percentiles with satellite lidar waveforms over the mountainous ar-eas is greatly challenged due to slanted and rugged topographic relief of underlying ground. A novel algorithm is proposed to extract the height percentiles based on the target response waveform (TRW) that is resolved by using a Richardson–Lucy deconvolution algorithm with an adaptive iterative time. The height metrics of the energy percentiles of 25%, 50%, 75% and 95% for the cumulative TRW distribution are determined by their vertical distances relative to the ground elevation in this study. To validate the proposed algorithm, we select the received waveforms of the Global Ecosystem Dynamics Investigation (GEDI) lidar over the Pahvant Mountains of central Utah, USA. The results reveal that the resolved TRWs resemble closely to the actual target response waveforms from the coincident airborne lidar data, with the mean values of the coefficient of correlation, total bias and root mean square error (RMSE) taking val-ue of 0.92, 0.0813 and 0.0016. In addition, the accuracies of the derived height percentiles from the proposed algorithm have been greatly improved compared with the conventional Gaussian de-composition method and the slope-adaptive waveform metrics method. The RMSE values de-crease by the mean values of 1.96 m and 2.72 m, respectively. It demonstrates that the proposed algorithm has good potential in the extraction of forest structure parameter over rugged moun-tainous areas.