Understanding long-term vegetation diversity patterns and their potential responses to climate and/or human driven processes are important for ecosystem modeling and conservation. Late-Holocene fossil pollen assemblage and associated vegetation diversity estimates provide an opportunity to explore the interactions among vegetation, climate, and human activities. A continuous 2000-year palynological record was obtained from the Beihai Wetland, southwestern China, to represent regional vegetation history, particularly the vegetation diversity changes. The results indicate that regional vegetation was dominated by deciduous broadleaved forest components (e.g. Alnus, deciduous Quercus), which showed a gradual decrease accompanied by expansion of herbaceous taxa (mainly Poaceae) after AD 800. Such progressive decline of forest was attributed to regional deforestation driven by intensified human activities, which was further confirmed by the increasing non-pollen polymorph abundance, particularly an abrupt rise after AD 1350. Vegetation diversity based on the Hill numbers ( N0, N1, and N2) showed a dramatic decline between ca. AD 200–400, which was triggered by regional fire events as shown by increased charcoal abundance from a nearby lake. The vegetation diversity reduced gradually after AD 800, especially the vegetation richness reflected by N0, revealing the transitional process from climate-driven to human-dominated vegetation changes. Minor increases of vegetation diversity occurred during Chinese dynastical transitions, probably due to reduced human activities following war-induced population crises. On the multidecadal scale, variations in vegetation diversity correlated significantly with climate fluctuations (revealed by synthesized temperature of China and stable oxygen isotope record from Dongge Cave) before AD 800, indicating a climate dominant condition. Then, the correlation between vegetation diversity and climate declined after AD 800, representing a progressive transition to human-dominant condition. In addition, the compositional turnover based on DCCA of the fossil pollen assemblage revealed a stepwise decrease, indicating reduced vegetation turnovers under anthropogenic influences.