Phenolic acids are abundant in rice straw (Oryza sativa L.). Exploiting the high value of phenolic acids (PAs) could solve the problem of straw resource utilization. For this, PAs were extracted from rice straw to investigate their antimicrobial effect in this study. Chemical composition of PAs was analyzed and 16 compounds were identified. The yield of PAs was 11.4 ± 0.4 g from 1 kg of rice straw, and the major compounds were p-coumaric acid (46.0%w/w), ferulic acid (23.3% w/w), vanillic acid (5.7% w/w) and vanillin (1.2% w/w). It was found that PAs had a strong inhibitory effect on Staphylococcus aureus in this study. The antimicrobial activity of PAs was mainly attributed to p-coumaric acid and ferulic acid. The minimum inhibitory concentration (MIC) values of p-coumaric acid and ferulic acid were 0.6 g/L and 1.2 g/L, respectively. More importantly, the combination of the phenolic acids could provide a synergistic effect. Therefore, the MIC of PAs derived from rice straw decreased by 1.5- to 3-fold relative to the MIC of p-coumaric acid and ferulic acid used individually. From assays of metabolites, adenosine triphosphate(ATP), adenosine diphosphate(ADP), oxidized form nicotinamide adenine dinucleotide(NAD+) and reduced form nicotinamide adenine dinucleotide(NADH), oxidized form nicotinamide adenine dinucleotide phosphate(NADP+) and reduced form nicotinamide adenine dinucleotide phosphate(NADPH), and the hydroxyl radical, the stimulation of the Fenton reaction was observed, which consumed adenosine triphosphate and reduced form of nicotinamide adenine dinucleotide, increased hydroxyl radicals, resulting in oxidative damage to cells, which was similar to the common mechanism of cell death induced by bactericidal antibiotics. Confocal laser scanning microscopic and atomic force microscopic images revealed that PAs destroyed the biofilm structure, changed the morphology of cells in the biofilm, and reduced their viability, suggesting potential medical applications for PAs. This study could provide theoretical guidance for the development of a plant-based antimicrobial agent, thus promoting straw utilization in a biorefinery.