This study conducted a series of experiments to investigate the degradation performance and mechanism of chlorpyrifos (CPF) degradation by Shewanella oneidensis MR-1 (S. oneidensis MR-1). The results showed that the S. oneidensis MR-1 degradation CPF rate was maximized at a salinity of 10g·L-1, 35 °C, pH 7, and an inoculum amount of 20%. The simultaneous addition of anthraquinone sodium 2,6-disulfonate (AQDS) and goethite [FeO(OH)] were able to increase the degradation efficiency to 174.12%. Further, SEM results showed the FeO(OH) surface might provide a dense reaction site for the degradation. XRD and FTIR analysis revealed the hydroxyl group participated in the degradation process. XPS analysis showed that the addition of AQDS and FeO(OH) promoted the conversion of Fe(III) to enhance the degradation of CPF. Meanwhile, metabolites analysis, indicated that S. oneidensis MR-1 regulated its antioxidant capacity by enhancing its amino acid metabolism and lipid biosynthesis to cope with CPF stress. This work could provide new insights for efficient CPF removal in the future.