A fishy odor can significantly hinder the development of products made from nutritious skipjack tuna. To address this issue, rosemary extract (RE) was used as a deodorizing agent for skipjack tuna. Multi-omics techniques, including e-nose, e-tongue, gas chromatography-ion mobility mass spectrometry (GC-IMS), and gas chromatography-mass spectrometry (GC-MS), were employed to analyze the volatile flavor compounds in the skipjack tuna meat before and after deodorization. The main fishy odors found in the skipjack tuna were identified as nonanal, heptanal, hexanal, and 1-octen-3-ol, primarily resulting from lipid oxidation. Treatment with RE solutions at concentrations of 0.8% and 1.0% completely removed nonanal, hexanal, and heptanal from the skipjack tuna meat, while the level of 1-octen-3-ol was significantly reduced by 67.21% (p < 0.05). The GC-MS analysis of the impregnated solution indicated a 31% increase in 1-octen-3-ol content at a concentration of 0.2% (p < 0.05). Additionally, skipjack tuna meat treated with 0.8% and 1.0% RE showed lower peroxide values and thiobarbituric acid reactive substances values (p < 0.05). The reduction of fishy odor by RE was directly linked to decreased lipid oxidation. Quantitative analysis of phenolics revealed that the relative content of phenolics in RE was 52.54%, with the main phenolics being chlorogenic acid, caffeic acid, and luteolin. Thus, RE shows promise in eliminating fishy odors and minimizing lipid oxidation in skipjack tuna.