Embryogenesis is a fantastic process during which a cell creates an organism. Our group takes systems biology approaches to investigate the regulatory mechanisms of animal embryogenesis using C. elegans. I will present our recent progresses towards multi-dimensional phenotypic and functional analysis of embryogenesis over time, space and genome. We have developed an automated phenotyping strategy to quantify developmental phenotypes of mutant embryos at single-cell resolution. It relies on long term 3D, time-lapse imaging of embryogenesis followed by transformation of 4D images into quantitative measurements of single cell’s developmental behaviors in terms of gene expression, proliferation, differentiation and morphogenesis. I will introduce the design and performance of our phenotyping strategy and explain how it facilitates large-scale analysis of phenotypes of every gene in every cell during every minute of embryogenesis. Furthermore, we have developed a general framework to transform massive phenotypic data into succinct and testable regulatory models of developmental regulation. I will introduce our recent work on dissecting the regulatory landscape of embryonic cell lineage differentiation. Through systems-wide perturbation and phenotypic inference we have revealed systems properties and multiscale models on how cell-specific gene networks drive cell differentiation along fate trajectories. Collectively, we provide a versatile systems biology platform to investigate the regulatory mechanisms, genetic networks and general properties of metazoan embryogenesis.