Exploring the geological events and climate change in the Himalaya-Hengduan Mountains (HHM) region and the Qinghai-Tibet Plateau (QTP) is crucial for understanding the impact of environmental change on biogeographic distribution and biological evolution. To delve deeper into these mechanisms, we reconstructed the evolutionary history of three Notholirion species that span these regions. Here, we examined a total of 254 individuals from 31 populations of these three species, utilizing five chloroplast DNA (cpDNA) (matK, ndhA, ndhG-ndhI, petB-petD, and petL-petG), along with one nuclear DNA region (internal transcribed spacer, ITS). We identified 14 haplotypes from cpDNA and 27 haplotypes from the ITS, each specific to corresponding species. Robust haplotype trees were detected, and obvious discrepancies were found between the cpDNA and ITS trees. A total of 147 chloroplast genomes were used for divergence time estimation, of which 10 chloroplast genomes from distinct populations of Notholirion species provided a comprehensive representation of the genus. The divergence time estimation results suggested that species of Notholirion genus originated in the southern Himalayan region during the Late Oligocene period (25.05 Ma), and the three Notholirion species then diverged during the Late Pliocene period (7.43 Ma). Our maximum model forecasts that the overall distribution range of Notholirion over four different periods remains relatively stable，from LIG to the future. The origin of the genus Notholirion was triggered by sustained climate fluctuations during the Late Oligocene, with the uplift of the Himalayas and the subsequent orogenic movements intensifying climate changes and further promoting the species divergence of Notholirion. A long evolutionary history, coupled with sexual reproduction and habitat fragmentation, likely contributed to the higher genetic diversity of Notholirion. The higher genetic differentiation among Notholirion populations may be attributed to drastic changes in the external environment within their range, as well as their constrained capacity for seed production and dispersal.