The Horqin Sandy Land in northeastern China is a critical ecological transition zone highly sensitive to climate change. However, the vegetation history and biodiversity dynamics of the Horqin Sandy Land remain insufficiently studied during the Holocene, which hinders a comprehensive understanding of the interplay between environmental changes and prehistoric human activities. In this study, we applied sedimentary ancient DNA analysis to perform high-resolution reconstructions of plant communities nearby the Haminmangha site, which is located in the center of the Horqin Sandy Land. The results showed that the Horqin Sandy Land has undergone three major phases of ecological changes from 5200 to 2400 cal. a BP. During the first phase (5200-4100 cal. a BP), the region was characterized by high plant diversity, a warm and humid climate, and minimal aeolian activity, which together supported the development of a forest-steppe ecosystem. In the second phase (4100-3600 cal. a BP), the climate became highly unstable, sand activity intensified, and plant diversity declined, indicating a transition toward cooler and drier conditions. In the final phase (3600-2400 cal. a BP), the climate further deteriorated with a transition to cooler and drier conditions, resulting in continued sand expansion, decreased plant diversity, and the formation of a typical sandy steppe environment. These ecological changes closely correspond to the trajectory of the Haminmangha Culture, in which favorable environmental conditions facilitated its development and interaction, whereas subsequent environmental deterioration likely contributed to its decline and the dispersal of its population. This study demonstratesthe utility of sedaDNA for reconstructing long-term ecological histories and provides a novel approach for investigating past human-environment interactions in northeastern China.