Photodynamic action of methionine-riboflavin mixture (MR) with a high level of reactive oxygen species (ROS) production is a powerful microbicidal system. Four important antioxidant proteins, including catalase, peroxidase, superoxide dismutase (SOD) and bovine serum albumin (BSA), were used to study the effects of MR photodynamic action on protein structure and enzymatic activity and to reveal the functional roles of ROS in MR toxicity. Protein structure damages by MR included degradation and cross-linking. All tested proteins were affected by MR and the level of degradation augmented as the length of the illumination treatment increased. Larger proteins were formed for catalase and SOD due to cross-linking following the MR treatment. Enzymatic activities of catalase, peroxidase and SOD decreased significantly in MR treatment at very early stage (15 min after illumination). Among the four proteins, SOD was the least sensitive protein to MR on both protein degradation and enzymatic activity reduction. Using ROS scavengers and ROS production promoters, ROS were demonstrated to be required for protein damages by MR. The damages of cellular important antioxidant proteins at a very early stage may result in the failure of cellular defense systems to oxidative stress and thus lead to cell death by MR.