Rare earth elements (REEs) accumulate in the soil and ecosystem. Cerium (Ce) is one of the main additives in REE-containing fertilizers. However, little information is available on Ce distribution patterns and chemical forms in rice. The subcellular distribution and chemical forms of Ce were investigated in the rice seedlings (Oryza sativa L., cv. Zhonghua 11) exposed to 0, 10, 20, 40, 80, and 160 μM Ce. The elongation of root and shoot was significantly inhibited by 20, 40, 80, and 160 μM Ce. Cerium was significantly accumulated in the cell walls, cell organelles, and soluble fractions of the roots and shoots with the increase of Ce concentrations. The concentrations of Ce in roots were significantly higher than shoots, and a large amount of Ce was stored in cell walls. In addition, Ce existed in the different chemical forms in the rice seedlings, and there were most insoluble oxalate or phosphate forms in roots. The subcellular distribution and chemical forms of Ce were closely associated with the metal tolerance and detoxification of rice.