Seed germination is a critical phase in rice production and is highly sensitive to environmental and chemical stresses. Chloramphenicol (CAM), a known phytotoxic antibiotic, has been reported to suppress rice seedling establishment, yet its underlying molecular mechanisms remain poorly understood. In this study, we investigated the effects of varying CAM concentrations on rice germination and early seedling establishment. While CAM significantly retarded germination speed and seedling growth, the final germination rates remained largely unaffected, even at high concentrations. To uncover the molecular basis of CAM phytotoxicity, we conducted time-resolved phosphoproteomic profiling during both the germination and early seedling stages. Our analyses revealed dynamic, stage-specific phosphorylation changes: moderate alterations affecting metabolic and cytokinesis-related processes during germination, and extensive disruptions in metabolic pathways, stress response mechanisms, DNA replication, and hormone signaling during early seedling establishment. Collectively, these findings demonstrate that CAM disrupts rice development by remodeling phosphorylation networks and modulating key physiological and signaling pathways. This study provides novel insights into the molecular mechanisms underlying antibiotic-induced growth inhibition and advances our understanding of plant stress responses during early development.