Cold atmospheric plasma (CAP) is considered to be a very promising cancer treatment method due to its “selective” killing effect on cancer cells. The 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 influence of the strong alternating electric field induced by CAP on the conformation and function of IL-6 remains unclear. In this study molecular dynamics simulation is used to investigate the effects of alternating electric fields with different frequencies and intensities on the conformation of IL-6. We statistically analyze 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 is utilized to assess the influence on the receptor-binding process. The results show that when the electric field frequency is below 30 MHz and the intensity exceeds 0.5 V/nm, the average dipole moment of IL-6 increases, leading to changes in the rigid regions at the C-terminus which 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 explains the internal interaction mechanism of CAP-induced electric fields affecting IL-6-related biological effects at the micro level, and provides important theoretical basis for optimizing parameters in the practical application of CAP in tumor inflammation treatment and the development of effective cancer therapy strategies.