As the most heavily used herbicide globally, glyphosate (GLY) has been detected in a variety of environments and has raised concerns about its ecological and health effects. There is debate as to whether GLY may disrupt the endocrine system. Here, we investigated the developmental toxicity of GLY in zebrafish based on deep learning-enabled morphometric analysis (DLMA). In addition, the estrogenic activity of GLY was assessed by endocrine disruption prediction, docking study and in vivo experiments. Results showed that exposure to environmental concentrations of GLY negatively impacted zebrafish development, causing yolk edema and pericardial edema. Endocrine disruption prediction suggested that GLY may target estrogen receptors (ER). Molecular docking analysis revealed binding of GLY to three zebrafish ER. In vivo zebrafish experiment, GLY enhanced the protein levels of ERα and the mRNA levels of cyp19a, HSD17b1, vtg1, vtg2, esr1, esr2a and esr2b. These results suggest that GLY may act as an endocrine disruptor by targeting ER, which warrants further attention for its potential toxicity to aquatic animals.