Iron (Fe) deficiency is a common challenge in crop production. Screening and research of Fe-efficient cultivars could alleviate plant stress and increase crop yields in Fe-deficient soils. In the present study, we conducted two hydroponic culture experiments with a control (100 μmol/L Fe3+-EDTA) and low Fe treatment (10 μmol/L Fe3+-EDTA) to study the morphological and physiological mechanisms of response to low Fe stress in maize hybrids seedlings. In the first experiment, we investigated 32 major maize hybrids in Southwest China. We found that six of them, including Zhenghong 2 (ZH 2), were Fe-efficient. Fifteen other cultivars, such as Chuandan 418 (CD 418), were Fe-inefficient. In the second experiment, we investigated the Fe-efficient ZH 2 and Fe-inefficient CD 418 cultivars and found that low Fe stress resulted in significant decreases in root volume, root length, number of root tips, root surface area, and root dry weight, and increased root to shoot ratio, average root diameter, and Fe-dissolution ability per mass of roots in both maize cultivars. However, the increase in Fe-dissolution ability per mass of roots in ZH 2 was higher than that in CD 418, whereas for the other measurements, the low Fe stress-induced changes in ZH 2 were less pronounced than in CD 418. Therefore, under low Fe stress, the above-mentioned growth factors in ZH 2 were higher by 54.84%, 121.46%, 107.67%, 83.96%, 140.00%, and 18.16%, respectively, than those in CD 418. In addition, leaf area, chlorophyll content, net photosynthetic rate, soluble protein content, and Catalase (CAT) and Peroxidase (POD) activities in ZH 2 were higher by 274.95%, 113.95%, 223.60%, 56.04%, 17.01% and 21.13% than those in CD 418. Therefore, compared with the Fe-inefficient cultivar (CD 418), the Fe-efficient cultivar (ZH 2) had a more developed root system and greater Fe absorption capacity per mass of roots under low iron stress, promoted the efficient absorption of Fe, maintained a higher photosynthetic area and photosynthetic rate, thereby facilitating the accumulation of photosynthetic products. Moreover, higher soluble protein content and activities of CAT and POD permitted high osmotic regulation and scavenging ability, which is an important physiological mechanism for ZH 2 adaptation to low Fe stress.