Sweetpotato (Ipomoea batatas L.) has great potential for combating micronutrient malnutrition and vitamin A deficiency. To explore the potential of combining different micronutrients in the same cultivar through genetic improvement, we assessed the variation of Fe and Zn contents among 21 genotypes and 5 growing locations in the eastern region of China. Large genotype-dependent differences for Fe and Zn were found in the storage roots. The Fe content ranged from 2.68 to 4.64 mg/100 g dry weight basis (dwb), whereas the Zn content ranged from 2.92 to 6.95 mg/100 g dwb. The variation caused by genotypes, locations, and genotype × environmental interaction was highly significant for both Fe and Zn. No significant correlation was found between β-carotene and Fe and Zn contents in the storage roots. The results show that sweetpotato as a staple or co-staple food may provide a good proportion of bioavailable Fe and Zn for the nutritional requirements of human populations. It appears feasible to increase Fe and Zn in orange-fleshed storage roots through breeding of new varieties.