Genetic variation is the most influential factor for carrot (Daucus carota L.) composition. However, difference in metabolite content between carrot varieties has not been described by NMR, although primary metabolites are important for human health and sensory properties. The aim of the present study was to investigate the effect of genotype on carrot metabolite composition using a (1)H NMR-based metabolomics approach. After extraction using aqueous and organic solvents, 25 hydrophilic metabolites, β-carotene, sterols, triacylglycerols, and phospholipids were detected. Multiblock PCA showed that three principal components could be identified for classification of the five carrot varieties using different spectroscopic regions and the results of the two solvent extraction methods as blocks. The varieties were characterized by differences in carbohydrate, amino acid, nucleotide, fatty acid, sterol, and β-carotene contents. (1)H NMR spectroscopy coupled with multiblock data analysis was an efficient and useful tool to map the carrot metabolome and identify genetic differences between varieties.