At a three-leaf stage, two Fe treatments [0 mg kg-1 (Fe-) and 20 mg.kg-1 (Fe+) in the form of FeCl3] were used in the soil of the pot and then two concentrations of α-ketoglutaric acid [0 mg L-1 (A-) and 50 mg L-1 (A+)] were sprayed to the rice plants of Meixiangzhan and Yuxiangyouzhan cultivars. We showed that seedlings exhibited an increased length and fresh and dry mass of shoots and roots with treatments Fe+A- and Fe-A+, as well as the Fe content increased greatly. Both treatments increased the morphological characteristic values of roots and promoted photosynthesis. Interestingly, Fe+A+ notably affected the photosynthesis of fragrant rice seedlings; however, it exerted no significant differences on other parameters. Overall, Fe and α-ketoglutaric acid had the potential for improving the growth of fragrant rice seedlings. The interaction between Fe and α-ketoglutaric acid regulated photosynthesis in seedling leaves, which provided evidence for further improvement of rice cultivation.