Abstract: Soybean protein is widely used as a high-quality plant protein in the food industry, due to its multiple functional properties. However, the high-activity lipoxygenase is easy to catalyze the lipid peroxidation of polyunsaturated fatty acids during the processing of soybean products. A large number of reactive oxygen species and secondary oxidation products can also be produced to further induce protein oxidation. The structure and function of proteins are closely related to the oxidation that is accompanied by the changes in protein solubility, water retention, gel, and emulsification functional properties, thus leading to the processing properties of proteins. Fortunately, microwave processing can be expected to alter the spatial structure of proteins and intermolecular forces. The reaction groups can be exposed to be originally embedded in the protein molecules, resulting in changes in their structure and functional characteristics. Taking the soybean protein oxidized aggregates as the raw materials, this work aims to clarify the effect of microwave treatment time on the functional characteristics and structure, such as solubility, emulsification, and foaming. The protein functional properties were then improved without the use of biochemical reagents, high-pressure, or radiation treatment, thereby expanding the protein applications without the wastes of food resources. An oxidization reaction was constructed with the soy protein and AAPH (2,2'-azobis(2-methylpropionamidine) dihydrochloride). Different irradiation durations (0, 10, 20, 30, 40, 50, 60, and 70 s) of the microwave with a power of 350 W were used to investigate the effect of microwave treatment on the structural characteristics (particle size distribution, turbidity, secondary structure, and microstructure) and processing properties (solubility, water-holding capacity, oil-holding capacity, foaming and foam stability, emulsification and emulsion stability) of oxidized aggregated soy protein. The results showed that the oxidation induced the formation of larger particle size, higher molecular weight, and more compact protein aggregates, which simultaneously damaged the processing properties. Microwave treatment for an appropriate time (<30 s) induced the polarization of protein isolate molecule. There was damage to the non-covalent bond that maintained the protein spatial structure. The protein isolate molecules were partially unfolded to expose the internal hydrophobic residues on the protein surface, thus promoting the formation of the water-air interface. At the same time, the interaction between that extensin molecules formed a more stable interfacial facial mask, thereby improving the foaming, emulsifying, water, and oil-holding properties. Microwave treatment for a long time (>30 s) promoted the further expansion of soy protein isolate molecules, and further exposure inside the hydrophobic and sulfhydryl groups. As such, the larger molecular aggregates were formed between depolymerized protein molecules through noncovalent bonds. There was an increase in the particle size, turbidity, and disordered structure, whereas, a decline in the stability of the interfacial facial mask, thus leading to the decline of functional properties. Consequently, the physical field of microwaves can be expected to modulate the functional properties of soy protein. Specifically, the structural and aggregation behavior can be altered to improve the functional properties of soy protein for the better behavior of soy protein oxidation aggregates using microwaves. The finding can also provide a strong reference for microwave processing in the field of food production.