This study investigated the effects of walnut phenolics and extraction methods on the composition and structural properties of walnut protein isolates (WPIs). Fluorescence quenching experiments showed that walnut phenolics could bind to walnut globulins, albumins, and glutelins with apparent affinity constants of 5.49 × 104 M-1, 1.71 × 104 M-1, and 3.10 × 104 M-1, respectively. However, the UV turbidity and dynamic light scattering (DLS) measurements indicated that phenolics could lead to the severe precipitation of globulins and albumins but not glutelins. The removal of pellicles could significantly increase the yield rate of salt-soluble globulins to approximately 72.8%. Furthermore, salt- and alkaline-extraction methods could produce comparable WPIs yields when using pellicle-free walnut kernels. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and size-exclusive chromatography indicated that the major protein compositions of the salt- and alkaline-extracted WPIs from pellicle-free walnut kernels were similar, while alkaline-extracted WPIs from kernels with pellicles exhibited phenolic-induced protein aggregation. Fourier transform infrared (FTIR) spectroscopy indicated that WPIs produced from kernels with pellicles contained more α-helix and less β-sheet structures than WPIs produced from pellicle-free kernels. These results confirm that walnut pellicle phenolics and the extraction methods could greatly influence the composition and structural properties of WPIs.