Phylogenetic structure is a key facet of biodiversity, reflecting the evolutionary history of species, and thus can be used to understand various ecological patterns. Although amphibian phylogenetic structures have been tested across space and time separately, simultaneous quantifications are still needed. In the present study, amphibians in streams of Tianping mountain, China, were selected as the model to investigate their elevational spatial and seasonal temporal patterns of phylogenetic diversity. Specifically, 13 streams located in lowland and highland sites were sampled for amphibians and measured for microhabitat variables in April, June, August, and October 2017, separately. Four phylogenetic structural indices, including Faith’s PD, standardized effect size (SES) of Faith’s PD, mean pairwise phylogenetic distance index (MPD), and SES.MPD, were calculated. Our results revealed that amphibian phylogenetic patterns were not significantly different between lowland and highland sites, but differed significantly between four seasons, associated with distinct community assembly rules (phylogenetically overdispersed vs. phylogenetically clustered). Importantly, these patterns were strongly determined by microhabitat variables such as rock cover, water temperature, and water depth. Our results provide fundamental knowledge to better protect amphibian diversity. Both elevational and seasonal variations are important to understanding the general patterns of amphibian community assembly rules.