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The growth of the Qinghai-Tibetan Plateau (QTP) during the Cenozoic drove dramatic climate and environmental change in this region. However, there has been limited comprehensive research into evolution of climate during this interval. Here we present a quantitative reconstruction using Bioclimatic Analysis (BA) and Joint Probability Density Functions (JPDFs) based on data available for 48 fossil floras, including macrofossils and palynological fossils collected in the QTP area from the Paleogene to Neogene (66–2.58 Ma). Both methods indicate that there was an overall decline in temperature and precipitation. Paleoclimatic simulations using Hadley Centre Coupled Model version3 (HadCM3) show that the most prominent climate change was very likely driven by QTP orographic evolution from the late Eocene, which was accompanied by a shift in temperature from a latitudinal distribution to a topographically controlled pattern. In addition, with the growth of the QTP, temperature and precipitation decreased gradually in the northeastern part of the plateau. Different sources of evidence, including plant fossil records, climate simulations and other proxies, indicate that the topographic evolution of the QTP and other geological events, in conjunction with global cooling, may have been the main factors driving climate change in this region. This research can provide insights into Cenozoic environmental change and ecosystem evolution.