In the present study, we measured spatiotemporal properties of ecological niches of amphibians in China and tested the relative importance of various niche-diversity metrics for explaining the evolutionary distinctiveness-weighted extinction risk (EDGE) of amphibian species. We applied the hierarchical partitioning technique on the phylogenetically independent contrasts of the niche covariates and EDGE of amphibians, for the purpose of removing the influence of evolutionary inertia among species. As a comparison, phylogenetic least-square general regression (PLGS) was also conducted. The results showed that EDGE was high for those amphibian species of China identified as Critically Endangered or Endangered on the IUCN Red List. Niche fragmentation dimension (NFD) and niche position (NP) were the top two predictors across partial correlation analyses, hierarchical variation partitioning, PLGS and multiple regression analyses. Most temporal niche properties were not significantly associated with the EDGE index of amphibians. Variation partitioning analysis showed that the spatial component of niche measures explained the largest proportion of total variation in EDGE (∼31%), whereas the temporal component of niche properties explained ∼8% of the variation. The significantly negative role of NFD and extinction risk of amphibians in China may be attributed to a reduced rescue effect, habitat geometry, and local extinction in species with large and continuous distributional ranges.