In the present study, we explored whether magnetic iron oxide nanoparticles (MNPs-Fe3O4) can be used to alleviate the toxicity of 3-nitrophenol (3-NP) to rice (Oryza sativa L.) seedlings grown under hydroponic conditions. The results showed that 3-NP from 7 to 560 μM decreased the growth, photochemical activity of the photosystem II (PS II), and chlorophyll content of the seedlings in a concentration-dependent manner. In the presence of 3-NP, 2,000 mg L−1 MNPs-Fe3O4 were added to the growth medium as the absorbents of 3-NP and then were separated with a magnet. The emergence of MNPs-Fe3O4 effectively alleviated the negative effects of 3-NP on rice seedlings. In addition, the long-term presence of MNPs-Fe3O4 (from 100 to 2,000 mg L−1) in the growth medium enhanced the growth, production of reactive oxygen species (ROS), activities of antioxidant enzymes, photochemical activity of PS II, and chlorophyll content of the rice seedlings. These results suggest that MNPs-Fe3O4 could be used as potential additives to relieve the physiological toxicity of 3-NP to rice seedlings.