This study investigated the differential effects of two thermal modifications, namely microwave (MW) and far-infrared radiation (FIR), on the structural and functional properties of zein. The results indicated that both modifications induced secondary structural rearrangement, with FIR exhibiting more pronounced regulatory effects than MW. All modified samples exhibited higher absorbance at 280 nm than the control group, indicating that the modifications promoted protein conformational unfolding, resulting in the exposure of aromatic amino acid residues. Microscopically, FIR-treated zein displayed a uniform lamellar structure, while MW-treated zein exhibited a porous network structure. Regarding functional properties, the sample treated with FIR at 100 ℃ demonstrated the best thermal stability (117.62 ℃), solubility (48.93%), water-holding capacity (47.05%), oil-holding capacity (54.97%), and emulsification activity index (29.75 m²/g), whereas that treated with MW at 800 W exhibited superior emulsion stability index (48.9 min), foaming capacity (82.46%), and foam stability (85.58%). In summary, FIR modification is more effective in enhancing protein thermal stability, solubility, water-holding capacity, oil-holding capacity, and interfacial emulsifying activity, while MW modification offers greater advantages in improving emulsion stability and foaming properties.