Phosphorus (P)‐hyperaccumulators for phytoextraction from P‐polluted areas generally show rapid growth and accumulate large amounts of P without any toxicity symptom, which depends on a range of physiological processes and gene expression patterns that have never been explored. We investigated growth, leaf element concentrations, P fractions, photosynthetic traits, and leaf metabolome and transcriptome response in amphibious P‐hyperaccumulators, Polygonum hydropiper and P. lapathifolium, to high‐P exposure (5 mmol L−1), with 0.05 mmol L−1 as the control. Under high‐P exposure, both species demonstrated good growth, allocating more P to metabolite P and inorganic P (Pi) accompanied by high potassium and calcium. The expression of a cluster of unigenes associated with photosynthesis was maintained or increased in P. lapathifolium, explaining the increase in net photosynthetic rate and the rapid growth under high‐P exposure. Metabolites of trehalose metabolism, including trehalose 6‐phosphate and trehalose, were sharply increased in both species by the high‐P exposure, in line with the enhanced expression of associated unigenes, indicating that trehalose metabolic pathway was closely related to high‐P tolerance. These findings elucidated the physiological and molecular responses involved in the photosynthesis and trehalose metabolism in P‐hyperaccumulators to high‐P exposure, and provides potential regulatory pathways to improve the P‐phytoextraction capability.