To evaluate the potential of defatted and dephenolized walnut meal as a modified functional food ingredient, this study examined how ball milling and processing time affect its structural, physicochemical, and functional properties. Walnut meal was ball-milled for 5, 10, 15, and 20 h. Ball milling increased the lightness and whiteness, reduced particle size, and broadened the particle size distribution into a characteristic three-peak pattern. Scanning electron microscopy revealed the progressive formation of flake-like surface structures. With increasing milling duration, free sulfhydryl groups, surface hydrophobicity, and solubility were increased, while dynamic surface tension decreased, leading to improved foaming capacity and foaming stability. SDS-PAGE confirmed that the primary structure remained unchanged, while Fourier transform infrared spectroscopy indicated a decrease in α-helix and β-sheet contents and an increase in random coil structures. X-ray diffraction revealed a reduction in the diffraction peak at 2θ = 8.963°, and differential scanning calorimetry showed irregular changes in the thermal stability with ball milling time. Overall, increasing ball milling time is beneficial for improving the functional properties of walnut meal, providing a preliminary theoretical reference for the potential application of walnut powder in foods with specific functional properties, such as aerated foods.