Satellite radar altimeters have been used to monitor sea level changes and ice sheet elevation changes for more than 3 decades. Over mountain glaciers, radar altimetry has limited applications due to contaminated radar waveforms caused by complex glacier surfaces and steep terrains. In this study, we develop a glacier-threshold method (GTM) to determine glacier elevation changes over mountain glaciers in Alaska. The GTM can detect and remove invalid elevation observations from the TOPEX/Poseidon (T/P) and Jason-2 (J2) altimeters, creating usable elevation observations from 16–92% of the raw observations. The selected elevations are used to construct long-term time series of Alaskan glacier elevation changes over 1993–2002 (T/P) and 2008–2016 (J2) at 47 sites. A crossover analysis and a Lidar comparison confirm the result from T/P and J2. Our finding shows that most of the Alaskan glaciers studied have continued to decline in recent years. The largest declining rate is -11.06 ± 0.35 m/yr over Klutlan Glacier, followed by Chitina Glacier at -8.82 ± 0.12 m/yr. Glacier thickening occurred in some accumulation zones, such as Hubbard Glacier and Logan Glacier, and also at some glacier terminuses. The mechanisms of these elevation changes are discussed using climate datasets. It is suggested that changes in environmental factors such as precipitation, air temperature and sea water temperature influence the shifts in the trends of glacier elevation changes. A sophisticated processing system and altimeter data from repeat missions can facilitate long-term monitoring of small-scaled glaciers for a better understanding of glacier dynamics.