This study aims to find the interaction between ionome and metabolome profiles of Pteris vittata L., an arsenic hyperaccumulator plant, to reveal its metal tolerance mechanism. Therefore, at the Pb-Zn mining sites located in Thai Nguyen province, Vietnam, where these species dominate, soil and plant samples were collected. Their multi-element compositions were analyzed using inductively coupled plasma mass spectrometry (ICP-MS) and thus referred to as the "ionomics" approach. In parallel, the widely targeted metabolomics profiles of these plant samples were performed using liquid chromatography-tandem mass spectrometry (UPLC-QqQ-MS). Nineteen elements, including both metals and nonmetals, were detected and quantified in both tissues of thirty-five plant individuals. A comparison of these elements' levels in two tissues showed that above-ground parts accumulated more As and inorganic P, whereas Zn, Pb, and Sb were raised mostly in the under-ground samples. The partial least squares regression (PLSR) model predicting the level of each element by the whole metabolome indicated that the enhancement of flavonoids content plays an essential contribution in adaptation with the higher levels of Pb, Ag, and Ni accumulated in the aerial part, and Mn, Pb in subterranean part. Moreover, the models also highlighted the effect of Mn and Pb on the metabolic induction of adenosine derivatives in subterranean parts. At the same time, the model presented the most contribution of As to the metabolisms of the amino acids of this tissue. On those accounts, the developed integration approach linking the ionomics and metabolomics data of P. vittata improved the understanding of the molecular mechanism of hyperaccumulation characteristics and provided markers that could be targeted in future investigations.