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Using molecular dynamics simulation with reactive force-field (ReaxFF), we study the reactive oxygen species (ROS)-mediated damage to the core domain of human immunodeficiency virus (HIV) integrase. Our results demonstrate that with the increase in the ROS concentration, the structure of the core domain of HIV is more severely damaged, including dehydrogenation, increasing oxygen-containing groups, shorting or damaging spirals, and breaking peptide bonds. We particularly note that ROS has a significantly higher capability to abstract H atoms from N atoms than C atoms. The effects of different species of ROS on dehydrogenation and shorting or damaging spirals are not prominent. In contrast, for increasing oxygen-containing groups and breaking peptide bonds, the effect of O is more remarkable than O3 and O3 is greater than ·OH. Moreover, carboxyl dehydrogenation and nitrogen dehydrogenation are more easily dehydrogenated, resulting in higher dehydrogenation ratios for polar amino acid residues. These meticulous findings deepen our understanding of the role of ROS in regulating the structure and function of the core domain of HIV integrase and provide valuable insights into the plasma treatment of acquired immune deficiency syndrome. [ABSTRACT FROM AUTHOR]