The linear mode laser altimeter onboard China's satellite is primarily used to provide elevation control points for imagery. During satellite operations, environmental variations can induce laser pointing offsets, which in turn increase the positioning errors of the footprints, thereby directly reducing the elevation accuracy of the control points. This issue is particularly pronounced in complex mountainous terrains. To enhance the reliability of laser altimeter observations from satellites in such regions, this paper proposed a new laser footprint positioning method based on waveform frequency domain matching. This method utilizes high-precision terrain data for waveform simulation and determines the position of the laser footprint by calculating the correlation between the simulated waveform and the waveform received by China's Gaofen series satellite in the frequency domain. Additionally, systematic deviations in laser pointing are derived from the joint computational results of multi-footprint frequency domain matching. Experiments were conducted using in three regions: central Montana, western Wyoming, and eastern Utah in the United States. The results indicate that the standard deviations of footprint planar offset distances, planar true north pinch angles, and equivalent laser pointing deviation angles obtained with this method are all superior to those achieved with the time-domain waveform matching method. The findings underscore the advantages of frequency-domain waveform matching in achieving high-precision footprint localization, thereby providing a robust foundation for enhancing the utility of satellite laser altimeter observations in challenging environments and facilitating the correction of laser altimeter pointing errors.