Shewanella oneidensis MR-1, a model strain of exoelectrogenic bacteria (EEB), plays a key role in environmental bioremediation and bioelectrochemical systems because of its unique respiration capacity. However, only a narrow range of substrates can be utilized by S. oneidensis MR-1 as carbon sources, resulting in its limited applications. In this work, a rapid, highly efficient and easily manipulated base editing system pCBEso was developed by fusing a Cas9 nickase (Cas9n (D10A)) with the cytidine deaminase rAPOBEC1 in S. oneidensis MR-1. The C-to-T conversion of suitable C within the base editing window could be readily and efficiently achieved by the pCBEso system without requiring double strand break or repair templates. Moreover, double-locus simultaneous editing was successfully accomplished with an efficiency of 87.5. With this tool, the roles of the key genes involving in N-acetyl-glucosamine (GlcNAc) or glucose metabolism in S. oneidensis MR-1 were identified. Furthermore, an engineered strain with expanded carbon source utilization spectra was constructed and exhibited a higher degradation rate for multiple organic pollutants (i.e., azo dyes and organoarsenic compounds) than the wild type when glucose or GlcNAc was used as the sole carbon source. Such a base editing system could be readily applied to other EEB. This work not only enhances the substrate utilization and pollutant degradation capacities of S. oneidensis MR-1, but also accelerates the robust construction of engineered strains for environmental bioremediation.