Whole oat milk (WOM) was prepared from germinated oat by an innovatively designed high-energy fluidic microfluidizer (HEFM). The results indicated that germination treatment significantly raised the content of total protein, γ-aminobutyric acid, total phenolics, and reducing sugar, while it decreased the content of total starch and β-glucan. Oat with a germination time of 48 h had the best nutritional quality for producing WOM. The physical stability of the WOM prepared from germinated oat was effectively improved by HEFM treatment. The apparent viscosity increased, the instability index reduced from 0.67 to 0.37, and the precipitate weight ratio decreased from 13.54% to 9.51%. As the pressure of the HEFM increased from 0 to 120 MPa, the particle size decreased from 169.5 to 77.0 µm, which was helpful to improve the physical stability of the WOM. Meanwhile, the color of the WOM became whiter after the HEFM treatment. The content of β-glucan and soluble protein in the WOM significantly increased, which was due to the disruption of cells by the HEFM processing. The optimal HEFM pressure for WOM production is 120 MPa. This study provided a new way to produce whole oat milk with a high nutritional quality and good physical properties.