Silkworm pupae proteins (SPP) have been exploited as a new functional protein, but there are still some people who are allergic to it. This study investigated the effects of different chemical modifications (phosphorylation, succinylation, deamidation, glycosylation) on SPP's allergenicity and its structural and functional impact. Spectroscopic analysis showed that all three modifications except glycosylation loosened the three-dimensional structure of SPP. Enzymatic hydrolysis studies have shown that the succinylated group can significantly enhance the hydrolysis resistance of SPP at 30 kDa, and the ability to bind IgE was maintained. Most proteins were hydrolyzed into small peptides within 30 min after combined digestion. A functional study of chemically modified SPP demonstrated that succinylation had a strong water-holding capacity. Further deamidation and phosphorylation have stupendous foaming ability and foaming stability, respectively. This discovery collectively will provide the experimental basis for developing and using silkworm pupae protein in the food industry.