As essential source for human consumption, plants of wheat, rice and soybean are highly sensitive to ozone (O3), resulting in significant agricultural losses under O3 pollution. However, little is known about the effects of elevated O3 on their metabolite profiling. In this study, three model cultivars were used for the metabolome analysis under elevated O3 and charcoal filtered air. Our study revealed that wheat and rice differed significantly from soybean in metabolic number and certain pathways. Metabolites response to elevated O3 were less in soybean, whilst those in wheat and rice were considerably larger. Under O3 stress, tricarboxylic acid cycle (TCA) was impaired in three crop plants. Methylerythritol 4-phosphate pathway and glycerol phosphate pathway were altered in wheat and rice with reduced terpene accumulation and high level of phospholipids. However, these pathways were not affected in soybean. Meanwhile, O3 suppressed the generation of flavonoid via benzoic acid pathway in three crop plants. Accordingly, the expressional level of genes coding key enzymes which catalyzed the synthesis or degradation of these metabolites. These findings provide valuable information for understanding of ozone’s effects on the metabolite profiling of crop plants, exploring the metabolite differences of three crop plants under elevated O3.