Shewanella baltica is a specific spoilage organism of golden pomfret. This study aims to explore the antibacterial mechanism of slightly acidic electrolysed water (SAEW) against S. baltica (strains ABa4, ABe2 and BBe1) in golden pomfret broths by metabolomics, proteomics and bioinformatics analyses. S. baltica was decreased by at least 3.94 log CFU/mL after SAEW treatment, and strain ABa4 had the highest resistance. Under SAEW stress, amino acids and organic acids in S. baltica decreased, and nucleotide related compounds degraded. Furthermore, 100 differentially expressed proteins (DEPs) were identified. Most DEPs of strains ABe2 and BBe1 were down-regulated, while some DEPs of strain ABa4 were up-regulated, especially those oxidative stress related proteins. These results suggest that the modes of SAEW against S. baltica can be traced to the inhibition of amino acid, carbon, nucleotide and sulphur metabolisms, and the loss of functional proteins for temperature regulation, translation, motility and protein folding.