Vegetation stability and biodiversity play a crucial role in maintaining the balance of the terrestrial ecosystem and the sustainable development of human beings. Since the distribution of modern vegetation and plant diversity is the result of long-term climate change and human activities, a long-term perspective on the trajectory and characteristics of changes in vegetation and plant diversity is an important basis for correctly predicting vegetation changes in the near future. In this study, we reconstructed the history of vegetation composition and plant diversity changes in the Erhai area over the past 400 years by analyzing pollen and sedimentary ancient DNA (sedaDNA) records from a 56-cm-long sediment core EH22s. The results showed that the numbers and types of plant taxa identified from pollen data (88 taxa) were very different from those identified from sedaDNA (204 taxa). In general, sedaDNA detected more plant taxa, and meanwhile, the detected taxa have better taxonomic resolution. However, of the more than 200 plant taxa identified from sedaDNA, only 38 plant taxa appear in pollen assemblages. This implies that the spatial scale of the vegetation reflected by pollen and sedaDNA is different, i.e. pollen reflects a regional scale while sedaDNA reflects a smaller scale like around the lake or within the catchment. The pollen records from the present study showed that the regional vegetation in the Erhai area had kept relatively stable despite significant climate change and human disturbances over the past 400 years, reflecting a strong ecological resilience in the regional vegetation. Climate change primarily affected plants with narrow ecological niche (e.g. Tsuga). Human activities exerted an obvious influence on the plants of Pinus, Alnus, and Poaceae by disafforesting natural forests and cultivating cash crops, which resulted in the expansion of secondary and economic forests and farmlands. sedaDNA record is able to reflect the vegetation conditions around the lake and can reflect trends in economic crops such as Oryza, Fagopyrum, Sorghum and Oryza sativa. Moreover, the vegetation changes around the lake or within the catchment revealed by sedaDNA were mainly influenced by human activities. In contrast to the relatively stable vegetation composition, both pollen and sedaDNA showed significant changes in plant diversity over the past 400 years, although their trends were not consistent. Besides, changes in plant diversity, both at the regional scale and around the lake, were mainly influenced by the mode and intensity of human activities. Based on the results, we suggest that pollen and sedaDNA record can complement each other in revealing changes in vegetation composition and plant diversity during the historical period, thus providing a more comprehensive assessment of past vegetation dynamics and an understanding of the potential mechanisms. In addition, considering that the plant diversity in the Erhai area is more sensitive to human activities, the vegetation conservation strategies in this region need to pay special attention to the changes in plant diversity.