Flavors are widely utilized in the food and oral pharmaceutical industry, particularly in products for children, to enhance palatability and promote ingestion willingness. The complex compositions of flavors potentially induce severer toxicity especially in children. In this study, zebrafish embryos are applied for toxicity screening of flavor and its compounds by immersing in flavor solutions followed by the assessment of morphology of zebrafish larvae. Geraniol is identified as the prominent toxic compound and is considered highly toxic to zebrafish embryo. In further toxicology study, geraniol demonstrates the concentration-dependent developmental toxicity as the obvious reduction of body and eye lengths, as well as the increased prevalence of tail deformities, pericardial edema, and spine deformation. Zebrafish larvae treated with geraniol exhibit reduction in liver area and exocrine pancreas length, increase in yolk sac area, as well as elevation of triglycerides and total cholesterol, which indicate the inhibited nutrient utilization. Transcriptome analysis reveals that under geraniol treatment, 248 differentially expressed genes (DEGs) are downregulated, whereas 23 DEGs are upregulated, and 110 DEGs are related to metabolic process. Biological processes of lipid metabolism, carbohydrate metabolism, protein hydrolysis, and transmembrane transport, including their involved functional genes, are all downregulated. These findings reveal the developmental toxicity of geraniol by affecting the nutrient utilization-related organs development and biological processes. This study establishes an efficient screening model for identifying toxic flavor compounds during developing stages, thereby elucidating the potential safety risks of geraniol exposure in zebrafish and providing a comprehensive understanding of its potential toxicity mechanism.