The principle of the Fourier transform is explored in this paper to compare protein structure similarity, transforming protein structure into a distance sequence, and performing spectral analysis on a fast Fourier transform. Secondly, protein fraction classification and similarity analysis of whole-seed wheat protein fractions were performed using the fast Fourier transform. Fourier transform infrared spectra were analyzed using two parameters: diatomic vibrations and molecular leaps. Finally, the whole seed wheat protein fraction content test analysis was analyzed experimentally. The results showed that the spectral range of whole seed wheat protein fractions was selected from 10539 cm−1 to 6080 cm−1, the fraction of fractions was determined as 9, the parameter R2 val was 0.9614. This paper provides practical reference material for researching whole-seed wheat protein fields.