A comprehensive understanding of the tectonic uplift history of the Tibetan Plateau (TP), a 2000 km wide region with a mean altitude of 4000–5000 m above sea level (asl), is crucial for interpreting global Cenozoic climate change, collisional tectonics and the evolution of the Asian climatic system. However, the timing, degree and extent of the uplift of the TP remain controversial. Here we report new palynological data from Early to Mid-Miocene lacustrine-swamp sediments in the Zeku Basin, northeastern TP. The palynoflora includes 68 palynotaxa at a family or genus level, comprising gymnosperms (16.2%), angiosperms (77.9%), pteridophytes (2.9%) and others (2.9%), and is suggestive of a mixed warm temperate forests of coniferous (e.g., Picea, Abies and Tsuga) and deciduous broadleaved trees (e.g., Ulmus/Zelkova, Betula and Quercus), with some subtropical elements (e.g., Carya and Liquidambar). Three periods of vegetation succession can be recognized from the Caergen Section, indicating a stepwise warming and drying trend from bottom to top. The local palaeoclimatic parameters obtained by applying the Coexistence Approach (CoA) to palynologic assemblages rendered mean annual temperature (MAT) values of 14.2–16.1 °C and mean annual precipitation (MAP) values of 797–1113 mm. This study departs from the traditional application of the CoA, relying on published determination of plant-climate relationships, rather than on data derived from the Paleoflora Database, which is currently not fully open-access. Based on the difference in temperatures between the Early to Mid-Miocene and the present day, and the temperature lapse rate, corrected to take account of Miocene global temperature differences, the estimated palaeoaltitude of the Zeku Basin during the Early to Mid-Miocene was 1200–1400 m asl. This palaeoaltitude estimate suggests that this basin has experienced about 2200–2500 m of uplift since the Early to Mid-Miocene. Findings therefore do not support previous hypotheses that the northeastern TP attained its present altitude before the Miocene.