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Background: Geographical distribution of endemic species and its multiple scale drivers are an important topic in biodiversity conservation, because these species are especially vulnerable to climate change and habitat degradation, and therefore have high conservation priority. Here, for the first time, we simultaneously linked glacial-interglacial climate change, contemporary climate, plant species richness and altitudinal range with endemic bird distribution in China. Methods: Ordinary least squares models and simultaneous autoregressive models were used to assess the associations between endemic bird richness, endemic bird ratio and each explanatory variable. Structural Equation Models were also performed to test the direct and indirect effects of these variables on endemic bird richness and endemic bird ratio. Results: Higher endemic bird richness and endemic bird ratio occurred in regions with stable glacial-interglacial temperature, i.e., southwest China. Plant species richness and altitudinal range were also positively correlated with endemic bird richness and endemic bird ratio. Glacial-interglacial temperature change, contemporary precipitation, plant species richness and altitudinal range were all included in the best combination of variables for endemic bird richness. Importantly, glacial-interglacial temperature change had strong direct effects on both endemic bird richness and endemic bird ratio, while plant species richness only had a direct effect on endemic bird richness. Conclusions: Our results indicate that endemic birds in China concentrate in southwest regions where there are stable glacial-interglacial temperature, more plant species and larger altitudinal range. Notably, while stable climate has strong direct effects on both endemic bird richness and endemic bird ratio, plant species may affect endemic bird richness through its effect on overall bird species richness. Importantly, the recent anthropogenic activities have also significantly intensified in this region, which would pose huge challenge for biodiversity conservation in China.