Heat shock protein 90α (HSP90AA1) is a molecular chaperone involved in a variety of cellular processes. Special attention is paid to how perillaldehyde ameliorates kidney injury by inhibiting HSP90AA1-mediated iron and pyrotoxicity, and in-depth analysis of the molecular structure and protein interactions of HSP90AA-1. The interaction between perillaldehyde and HSP90AA1 and the effect of perillaldehyde on the molecular structure of HSP90AA1 were analyzed by molecular docking and surface plasmon resonance technique. Western blot and immunohistochemical results showed that perillaldehyde could decrease the expression of HSP90AA1 and change its distribution in the kidney. Molecular docking and surface plasmonic resonance experiments revealed the high affinity binding between perillaldehyde and HSP90AA1, and further analysis showed that perillaldehyde could induce the conformational change of HSP90AA1, thereby inhibiting its function.