Cold Atmospheric Plasma (CAP) is considered to be a highly promising cancer treatment method due to its "selective" killing effect on cancer cells. CAP can inhibit tumor inflammatory responses and activate the immune system by reducing the expression of the key inflammatory factor Interleukin-6 (IL-6). However, the impact of the strong alternating electric field induced by CAP on the conformation and function of IL-6 remains unclear. This study employs molecular dynamics simulations to investigate the effects of alternating electric fields with different frequencies and intensities on the conformation of IL-6. We statistically analyzed the root mean square fluctuations, root mean square deviation, secondary structural alterations, and dipole moment changes of IL-6 under different electric field parameters. Furthermore, molecular docking was utilized to assess the impact on the receptor-binding process. The results demonstrated that when the electric field frequency was below 30 MHz and the intensity exceeded 0.5 V/nm, the average dipole moment of IL-6 increases, leading to changes in the rigid regions at the C-terminus that maintain structural stability. Specifically, the salt bridges that stabilize the long helices rupture, and the number of α-helices decreases. The docking outcomes reveal that the distance between the key binding residues of the conformationally altered IL-6 and its receptor increases, thereby disrupting the normal binding process and potentially impairing its normal biological functionality. This study provides a microscopic explanation of the internal interaction mechanisms by which CAP-induced electric fields influence IL-6-related biological effects. The findings offer crucial theoretical insights for parameter optimization in the practical application of CAP for tumor inflammation treatment and the development of effective cancer therapy strategies.