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Vertebrate embryogenesis is a remarkable process, during which numerous cell types of different lineages arise within a short time frame. An overwhelming challenge to understand this process is the lack of dynamic chromatin accessibility information to correlate <em>cis</em>-regulatory elements (CREs) and gene expression within the hierarchy of cell fate decisions. Here, we employed single-nucleus ATAC-seq to generate a chromatin accessibility dataset on the first day of zebrafish embryogenesis, obtained 51,620 high-quality nucleis and 23 clusters, and dissected the distinct differences in chromatin accessibility during blastula, gastrula and segmentation. By integrating ATAC-seq with single-cell RNA-seq data, we described the dynamics of chromatin accessibility and gene expression across developmental time, which exhibits that chromatin accessibility precedes the expression of genes at early stages. Furthermore, we identified cell-type-specific CREs and the potential enhancers that might be essential for tissue differentiation at gastrula and segmentation. Together, our data could serve as a fundamental resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis.