The tree of life (TOL) is severely threatened by climate and land-cover changes. Preserving the TOL is urgent, but has not been included in the post-2020 global biodiversity framework. Protected areas (PAs) are fundamental for biological conservation. However, we know little about the effectiveness of existing PAs in preserving the TOL of plants and how to prioritize PA expansion for better TOL preservation under future climate and land-cover changes. Here, using high-resolution distribution maps of 8732 woody species in China and phylogeny-based Zonation, we find that current PAs perform poorly in preserving the TOL both at the present and in the 2070s. The geographical coverage of TOL branches by current PAs is ca. 9%, and < 3% of the identified priority areas for preserving the TOL are currently protected. Interestingly, the geographical coverage of TOL branches by PAs will be improved from 9% to 52–79% by the identified priority areas for PA expansion. Human pressures in the identified priority areas are high, leading to high costs for future PA expansion. We thus suggest that besides nature reserves and national parks, other effective area-based conservation measures should be considered. Our study argues for the inclusion of preserving the TOL in the post-2020 conservation framework and provides references for decision-makers to preserve the Earth’s evolutionary history.