Climate warming and engineering activities have various impacts on the thermal regime of permafrost in alpine ecosystems of the Qinghai–Tibet Plateau. Using recent observations of permafrost thermal regimes along the Qinghai–Tibet highway and railway, the changes of such regimes beneath embankments constructed in alpine meadows and steppes are studied. The results show that alpine meadows on the Qinghai–Tibet Plateau can have a controlling role among engineering construction effects on permafrost beneath embankments. As before railway construction, the artificial permafrost table (APT) beneath embankments is not only affected by climate change and engineering activities but is also controlled by alpine ecosystems. However, the change rate of APT is not dependent on ecosystem type, which is predominantly affected by climate change and engineering activities. Instead, the rate is mainly related to cooling effects of railway ballast and heat absorption effects of asphalt pavement. No large difference between alpine and steppe can be identified regarding the variation of soil temperature beneath embankments, but this difference is readily identified in the variation of mean annual soil temperature with depth. The vegetation layer in alpine meadows has an insulation role among engineering activity effects on permafrost beneath embankments, but this insulation gradually disappears because the layer decays and compresses over time. On the whole, this layer is advantageous for alleviating permafrost temperature rise in the short term, but its effect gradually weakens in the long term.