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The effects of marine Streptomyces on the corrosion process of X65 steel were investigated by a complete characterization of metabolites using untargeted metabolomics, combined with surface analysis and electrochemical measurements. The results showed that the organic acid produced by Streptomyces accelerated the average corrosion rate of X65 steel in the early stage, but the formation of special “honeycomb” corrosion product structure promoted the enrichment of protein/polysaccharide in metabolites on the metal surface in the middle stage, and the biomineralized film was denser, which slowed down the corrosion especially localized corrosion. In the later stage, the corrosion was intensified due to the shedding of the protective film layer, but no obvious pitting corrosion was observed. In addition, the unique antimicrobial-like metabolites have potential applications in the field of microbiologically influenced corrosion inhibition by microbial control methods.