A major challenge in understanding vertebrate embryogenesis is the lack of topographical transcriptomic information that can help correlate microenvironmental cues within the hierarchy of cell-fate decisions. Here, we employed Stereo-seq to profile 91 zebrafish embryo sections covering six critical time points during the first 24 h of development, obtaining a total of 152,977 spots at a resolution of 10 × 10 × 15 μm3 (close to cellular size) with spatial coordinates. Meanwhile, we identified spatial modules and co-varying genes for specific tissue organizations. By performing the integrated analysis of the Stereo-seq and scRNA-seq data from each time point, we reconstructed the spatially resolved developmental trajectories of cell-fate transitions and molecular changes during zebrafish embryogenesis. We further investigated the spatial distribution of ligand-receptor pairs and identified potentially important interactions during zebrafish embryo development. Our study constitutes a fundamental reference for further studies aiming to understand vertebrate development. [Display omitted] • Stereo-seq is used to generate a ZESTA • Co-varying spatial gene modules reveal the interactions between functional regions • Integration of Stereo-seq and scRNA-seq builds spatial developmental trajectories • Spatiotemporal ligand-receptor dynamics provides insights to regulatory mechanisms Liu et al. employ Stereo-seq to dissect the spatiotemporal transcriptomic dynamics in developing zebrafish embryos. This study provides a spatially resolved resource for the research of vertebrate embryogenesis and also helps to uncover how molecular and cellular interactions contribute to zebrafish embryogenesis. [ABSTRACT FROM AUTHOR]