Current marine mackerel (Scomberomorus niphonius) products predominantly involve low-value-added processing, while high-value-added products like fish floss remain underdeveloped. This study utilized mackerel dorsal muscle treated with flavor protease (FP), papain (PP), and neutral protease (NP) (10 U/g, 30 min), followed by steaming and stir-frying. Combined with sensory evaluation, HS-GC-IMS, and automatic amino acid analysis, the characteristic flavor was evaluated by multi-omics. The results showed that FP and NP significantly enhanced odor by reducing fishy compounds (e.g., hexanal) and increasing pyrazines/furans. PP enhanced taste by elevating umami and sweet amino acids (26.68% and 25.98%, respectively). Correlation analysis revealed the following potential pathways: Val and Leu served as precursors for furan, suppressing 2-methyl-3-(methylthio)furan formation, while Asp, Tyr, Phe, Gly, Cys, and Ile promoted 2,5-dimethylpyrazine and 2-methyl-3-(methylthio)furan generation while inhibiting furan. This study demonstrates that minimal protease addition effectively optimizes dried mackerel floss flavor, providing a novel approach for high-quality marine product development.