The study investigates the impacts of indigenous bacterial strains inoculation specifically L. pentosus, on the flavor characteristics, microbial composition, and metabolite profiles of fermented oyster hydrolysates. This research aimed to elucidate potential mechanisms underlying the reduction of off-flavors in fermented hydrolysates. A total of 46 and 57 volatile compounds were detected by GC-MS and GC-IMS in hydrolysates inoculated with different core microbes, respectively. The 9 key volatile compounds detected by GC-MS analysis. (E, E)-2,4-heptadienal, heptanal, octanal, pentanal, and (E)-2-octenal reduced the off-flavor of the fermented oyster hydrolysate. Meanwhile 1-octen-3-ol, 3-octanone, 4-octanone, and (E, Z)-2,6-nonadienal enhanced the direct contribution of desirable flavors. Variation in 16 amino acids, 10 organic acids and 3 nucleotides were monitored to further understand the metabolic changes affecting flavor quality. Moreover, pyruvate decarboxylase [EC 4.1.1.1], phosphomannanase [EC 3.2.1.109], lipoyl-CoA synthetase [EC 6.3.2.4], and arginine kinase [EC 2.7.3.3] were the main microbiologically active enzymes. An increase in the content of aromatic compounds and a decrease in the content of C6-C9 unsaturated aldehydes through Lys, Phe, Asp, Glu, phosphoenolpyruvate, oleic acid, and linoleic acid metabolism pathways improved the flavor of oyster hydrolysates fermented by L. pentosus. This research provides a theoretical basis for leveraging autochthonous microbial fermentation to systematically improve flavor characteristics in fermented products.