We have investigated the mechanism of plasma‐induced water pore formation in model 1,2‐dioleoyl‐sn‐glycero‐3‐phosphocholine (DOPC) bilayer membrane systems using atomistic molecular dynamics (MD) simulations. Oxidized by reactive oxygen species generated upon the plasma treatment, unsaturated hydrocarbon tails of DOPC lipids are converted into shortened hydrocarbon tails with terminal groups such as peroxide or aldehyde. Among them, the lipids with both hydrocarbon tails oxidized into aldehyde groups are particularly susceptible to the stable water pore formation. By analyzing the water pore formation dynamics, lipid escape, and lipid clustering for the plasma‐damaged DOPC membrane systems, we have found that a stable water pore is formed in the membrane region where the plasma‐damaged lipids are highly concentrated or locally clustered. In the plasma‐damaged lipid‐rich region, a continuous water channel through the membrane is easily established with the help of the terminal aldehyde groups in the tails of damaged lipids, and it continuously grows with time to form a stable water pore. The rapid local clustering or domain formation of the plasma‐damaged lipids is due to both the hydrophobic mismatch between normal and oxidized DOPC lipids and enhanced lateral diffusion of the oxidized lipids in the membrane. We have also observed that the onset concentration of oxidized lipids for the stable water pore formation is approximately 30% in the model DOPC membrane systems.