Cold atmospheric plasma (CAP) is considered to be a highly promising cancer treatment method, due to its “selective” anti-cancer effect. However, the physical theoretical explanation about this effect and the microscopic interactive mechanisms between CAP and tumors are still lacking. In this work, the CAP-induced electric field-caused electroporation (EP) processes of the cell membrane are modeled based on molecular dynamics. Additionally, the umbrella sampling method is utilized to compute the free energy profile of the intracellular permeation processes of the reactive oxygen species (ROS) through EP-formed pore-like structures at different EP stages. Comparative results are shown as follows. 1) Cancer cell membranes with lower cholesterol components show lower EP-generation threshold and faster EP-formation, and 2) lower free-energy barrier and earlier occurrence of free-energy barrier reduction are shown in all EP stages in cancer cell membrane. The above results explain the difference between cancer cells and normal cells when affected by CAP. Our work delves into the formation of CAP-induced EP and the transport of ROS through EP-formed pore-like structures, which contributes to a better understanding of the microscopic mechanisms of the “selective” anti-cancer effect of CAP, and provides important references for developing CAP-based cancer treatment methods, and devices, thereby facilitating the translation of CAP into clinical applications.