On September 15, 2018, NASA successfully launched the ICESat-2 satellite, which carries the Advanced Topographic Laser Altimeter System (ATLAS). ATLAS/ICESat-2 has been widely used in many research fields, such as polar ice-sheet elevation measurement, sea-ice thickness estimation, land elevation measurement, and vegetation measurement. Unlike GLAS/ICESat, ATLAS uses a more sensitive single-photon detector in the signal detection system. The system emits 10 000 pulses per second (GLAS/ICESat system emits 40 pulses per second), which enables high-density photon data with higher repetition frequency and smaller light spots, thus enabling high-precision global observation. Due to the influence of the detector photomultiplier tube (PMT) after-pulse used by ATLAS, small amplitude pulse interference often occurs after the output of echo signal pulse, which cannot accurately reflect the original signal waveform. Therefore, the measured signal must be corrected in the practical application process. Firstly, based on ATL03 product, the photon counting echo data were preprocessed to obtain the profiles of sea ice, ocean, land and desert. The results show that there are two small pulse echoes (about 2.3 m and 4.2 m) after the main signal echo, and there is a longer delay pulse echo between land and desert (about 10-45 m). It is confirmed that different reflective surfaces are affected by after-pulse of PMT. Secondly, the impulse response functions under different beams were calculated by using the night observation data of ICESat-2 over the Sahara Desert. The overall shape of the impulse response functions obtained from the six beams was similar. After the main signal echo, there were three pulse echoes of different amplitude (about 2.3 m, 4.2 m and 6.5 m). Finally, the impulse response functions under six beams were used to correct the same ocean profile. The results show that except ATLAS Beam2, all the other beams can effectively filter out the small amplitude pulse after the main pulse, and the real underwater echo signal can be picked up.