The application of physical processing technologies in fermentation is an effective way to improve the quality of substrates. The purpose of the study was to evaluate the feasibility of enhancing the polypeptides of rapeseed meal (RSM) by a low-intensity alternating magnetic field (LF-MF)-assisted solid-state fermentation. A protease-producing strain B16 from RSM was isolated and identified as by analyzing its morphology and 16S rDNA sequencing. Then, it was employed in solid-state fermentation for polypeptide production. The results showed that the neutral protease activity could reach 147.48 U/mL when was cultured under suitable conditions. The protease activity increased rapidly on the 2.5th day of traditional fermentation, while the polypeptide yield reached the maximum on the third day. The highest polypeptides content was achieved by LF-MF-assisted fermentation at magnetic field intensity 140 Gs, treatment 4 h, magnetic field intervention after 16 h of inoculation, and rotation speed 50 rpm/min, which increased by 18.98% compared with traditional fermentation. Therefore, LF-MF-assisted fermentation effectively enhanced the polypeptide yield. The results suggested that LF-MF technology would be widely used to produce bioactive components from agro-industrial by-products.