The effects of different extraction methods on the contents of disulfide (SS) and sulfhydryl (SH) and secondary structure of albumin, globulin, prolamin and glutelin fractions from walnut proteins were evaluated. By comparison with the changing trend for four protein fractions from alkali extraction with isoelectric precipitation (AEIP), the SH contents of globulin, prolamin and glutelin fractions from the reverse micelles (RMs) significantly increased (p < 0.05), but decreased in the albumin faction. The SS bond contents of albumin, globulin and glutelin fractions obtained by two extraction methods were similar, except that the SS bond content in prolamin obtained through RMs increased by 2.57%. Fourier transform infrared (FTIR) results showed that the proportions of α–helix in globulin, β–sheet structure in prolamin, unordered structure in globulin, prolamin and glutein, turn structure in albumin, prolamin and glutelin by RMs were higher than those by AEIP. Scanning electron microscopy showed that the reverse micelle extraction could affect the surface structures of four protein fractions.