Ginkgo (Ginkgo biloba L.) is not only considered a ‘living fossil’, but also has important ecological, economic, and medicinal values. However, the impact of climate change on the performance and distribution of this plant is an increasing concern. In this study, we developed a bioclimatic model based on data about the occurrence of ginkgo from 277 locations, and validated model predictions using a wide-ranging field test (12 test sites, located at the areas from 22.49° N to 39.32° N, and 81.11° E to 123.53° E). We found that the degree-days below zero were the most important climate variable determining ginkgo distribution. Based on the model predictions, we classified the habitat suitability for ginkgo into four categories (high, medium, low, and unsuitable), accounting for 9.29%, 6.09%, 8.46%, and 76.16% of China’s land area, respectively. The ANOVA results of the validation test showed significant differences in observed leaf-traits among the four habitat types (p < 0.05), and importantly the rankings of the leaf traits were consistent with our classification of the habitat suitability, suggesting the effectiveness of our classification in terms of biological and economic significance. In addition, we projected that suitable (high and medium) habitats for ginkgo would shrink and shift northward under both the RCP4.5 and RCP8.5 climate change scenarios for three future periods (the 2020s, 2050s, and 2080s). However, the area of low-suitable habitat would increase, resulting in a slight decrease in unsuitable habitats. Our findings contribute to a better understanding of climate change impact on this plant and provide a scientific basis for developing adaptive strategies for future climate.