The tea plant is a fluoride (F) and aluminum (Al) hyperaccumulator. High concentrations of F and Al have always been found in tea leaves without symptoms of toxicity, which may be related to the special localization of F and Al in tea leaves. In this study, we for the first time determined the subcellular localization of F and Al in tea roots and leaves and provided evidence of the detoxification mechanisms of high concentrations of F and Al in tea plants. Results revealed that 52.3 and 71.8% of the total F accumulated in the soluble fraction of tea roots and leaves, and vacuoles contained 98.1% of the total F measured in the protoplasts of tea leaves. Cell walls contained 69.8 and 75.2% of the total Al detected in the tea roots and leaves, respectively, and 73.2% of Al sequestered in cell walls was immobilized by pectin and hemicellulose components. Meanwhile, 88.3% of the Al measured in protoplasts was stored in the vacuoles of tea leaves. Our results suggested that the subcellular distributions of F and Al in tea plants play two important roles in the detoxification of F and Al toxicities. First, most of the F and Al was sequestered in the vacuole fractions in tea leaves, which could reduce their toxicities to organelles. Second, Al can be immobilized in the pectin and hemicellulose components of cell walls, which could suppress the uptake of Al by tea roots.