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Vernalization is the process that accelerates flowering by prolonged winter cold, which maximizes the reproduction of plants in the favorable condition in spring. Decades of genetic and biochemical studies in Arabidopsis thaliana have uncovered various components in vernalization pathway. Considering the environment-dependent and quantitative nature of vernalization response, comprehensive profiling of the transcriptome and epigenome dynamics of this process would undoubtedly help us understand the underlying connections and regulatory mechanisms. However, despite intensive applications of next-generation sequencing in diverse aspects of plant research, few genome-wide sequencing data on vernalization response is available to date. In this work, we present the first comprehensive analysis of time-series transcriptome and epigenome changes during vernalization process in Arabidopsis thaliana. Six major clusters of genes with distinctive transcriptome dynamics were identified, and corresponding enriched motifs indicated the connection between hypoxia and vernalization pathways. Epigenetic analysis revealed a temporal change of histone H3K4me3 modifications during long-term cold to coordinate photosynthesis and prevent oxidative damage in plants. Meanwhile, vernalization induced a stable enrichment of H3K27me3 in a large portion of development-related transcription factors, resulting in either switch-off or bivalent status that functions to promote differentiation and phase transition. Lastly, we predicted FLC- and VIN3-like genes with similar transcriptional dynamics during vernalization which would help us in understanding the regulatory mechanisms