Chromatin-based organization of the eukaryotic genome plays a profound role in regulating gene activity. Nucleosomes form the basic subunits of chromatin by packaging DNA with histone proteins, impeding the access of DNA to regulatory proteins and RNA polymerases. The exchange of histone variants alters the properties of nucleosomes, which in turn affect chromatin organization and transcription. In plants, histone H3 variants exhibit similar specialized properties as their animal counterparts, though they evolved independently in animals and plants, suggesting evolutionary convergence. One of the histone H3 variants, H3.3, acts as a replacement histone and is closely linked to transcriptional activation. However, the detailed function of H3.3 in plant chromatin regulation remains elusive. Here, we reveal that H3.3 is essential for endowing seeds with post-embryonic developmental potentials. H3.3 exhibits a seed-specific 5′ gene end distribution pattern and facilitates chromatin opening at regulatory regions in seeds. During germination, H3.3 is essential for proper gene transcriptional regulation. In addition, we demonstrate that H3.3 promotes plant response to warm temperatures (i.e. thermomorphogenesis), including the induction of RNA Pol II transcription under warm conditions, and its deposition is closely coordinated with the eviction of another histone variant H2A.Z from the chromatin. Together, our findings highlight the importance of histone variants in programming transcription during developmental transitions and environmental responses.