Long‐term climate stability is hypothesized to drive the emergence of species assemblages with large species age differences due to the accumulation of relict species and relatively newly arisen species via reduced extinction and increased speciation. Few studies have addressed these predictions and so far no study has done so for plants across the Northern Hemisphere. Here, we linked Quaternary‐scale climate variability to phylogenetic age differences between the oldest and youngest group of species in tree assemblages in 100 km × 100 km grid cells across the Northern Hemisphere to test these predictions. Last Glacial Maximum (LGM)‐to‐present shifts in temperature and precipitation were used as proxies for Quaternary‐scale glacial–interglacial climate variability. Simultaneous autoregressive (SAR) models were used to assess the relationships between phylogenetic age differences and Quaternary‐scale climate variability. We found that phylogenetic age differences overall were largest in China and smallest in Europe, and they declined with increasing temperature instability as predicted, but only in Europe and North America. In China, the relatively mild Quaternary climate changes did not appear to have strongly affected phylogenetic age differences in tree assemblages. Our results show that phylogenetically diverse assemblages with large phylogenetic age differences among species are associated with relatively high long‐term climate stability, with intra‐regional links between long‐term climate variability and phylogenetic composition especially strong in the more unstable regions. These findings point to future climate change as a key risk to the preservation of the phylogenetically diverse assemblages in regions characterized by relatively high paleoclimate stability, with China as a key example.