Traditional heat extraction (HE) has a low efficiency (75.2 wt%) and induces lipid oxidation of PUFAs. The novel micro-aqueous cold (<25 °C) extraction (MAE) was applied to extract salmon head oil. The recovery rate was 93.4 wt% at oil volume fraction Φ = 74 %. The extraction mechanism was agitation-induced droplet coalescence at an unstable and close-packing state (Φ = 74 %), increasing the portions of the large-sized droplets (>50 μm) from 2.8 vol% to 91.7 vol%. The MAE reduced the oil oxidation level and odor intensity compared to HE, although the lipid profile differed slightly. The HE head oil had more key fishy odor compounds, including hexanal (0.98 mg/kg), 3-methyl-butanal (0.25 mg/kg), 1-penten-3-ol (0.49 mg/kg), and 2-ethylfuran (0.19 mg/kg). The MAE oil had only 2-methyl-butanal (0.10 mg/kg) and 1-penten-3-ol (0.47 mg/kg). Overall, micro-aqueous extraction has great potential to replace industrial heat extraction with a better product quality.