Chitosan oligosaccharide (COS) has multiple biological properties and is hence promising in the modification of proteins through Mallard reaction. Its susceptibility to the reaction with soybean protein isolate (SPI) was evaluated by comparing with glucose (Glu). Conjugation with COS led to milder color change, less furosine and hydroxymethyl furfural formation, and fewer lysine/arginine consumption than with Glu, implying that COS was less susceptible to the Maillard reaction with SPI than Glu. Intrinsic fluorescence analysis indicated that different intermediate products were generated in the SPI-Glu and SPI-COS conjugates and the former intermediates were more prone to condensation to brown pigments. SDS-PAGE illustrated that COS inclined to conjugate with the small subunits of SPI. Conjugation with COS caused SPI unfolding and improved its emulsifying activity. Hence, COS has great potential in the modification of proteins through Maillard reaction and other attributes of the resultant conjugates, such as antioxidant and antibacterial activities, deserve further study.