Utilizing wheat embryos as the raw material and employing Aspergillus niger as the fermentation strain, wheat embryo polypeptides were produced through microbial liquid fermentation. The protein concentration post-fermentation served as the response variable, and the preparation process underwent optimization through single-factor testing and a response surface methodology, followed by the assessment of antioxidant activity. The findings revealed that the optimal conditions for wheat embryo peptide preparation via Aspergillus niger fermentation included a fermentation duration of 24 h, an inoculum volume of 4%, an initial pH of 7, and a protein concentration of 21.47 mg/mL. Peptides with different molecular weights were then prepared by dead-end filtration. The results showed that F6 (<3 kDa) had strong scavenging ability against DPPH, ABTS, and ·OH radicals, which provided a basis for the preparation of antioxidant peptides in wheat germ and related research.