Phytoremediation, which is a plant-based technology for the removal of toxic contaminants from soil, has been receiving renewed attention as an environmentally friendly purification method. In this work, phytoremediation of soil contaminated with heavy metals and a novel recovery method of valuable metals were investigated. Athyrium yokoscense was used as a hyperaccumulating plant. The plants were separated into water-soluble material, holocellulose, methanol-soluble lignin (low-molecular-weight lignin), and Klason lignin (high-molecular-weight lignin) using steam-explosion and Wayman's extraction method, and the concentrations of metals, i.e., copper and iron, were measured. Levels of 15 mg of copper and 2.6 mg of iron were found in 1 g of the water-soluble material component of aboveground parts, i.e., leaf blades and petioles; and 41 mg of copper and 4.2 mg of iron in 1 g of the Klason lignin (high-molecular-weight lignin) component of underground parts, i.e., rhizomes and roots. This suggests that these components can be used for recovery of metals. The amounts of heavy metals in contaminated soil and plants were estimated. It was found that 1 g of copper and 0.1 g of iron were recovered from 500g of contaminated soil, and the removal ratios of copper and iron in the contaminated soil were 82 and 95%, respectively.