At present, the structure−activity relationships of soy protein isolate are still not well understood. In this paper, the relationship between molecular flexibility and emulsifying properties of soy protein isolate and soy protein isolate−glucose conjugates were investigated. The Maillard reaction was carried out at different temperature conditions (50 °C, 60 °C, 70 °C, 80 °C, and 90 °C) under a specific wet condition. Meanwhile, structural properties including surface hydrophobicity (H 0 ), molecular flexibility and secondary, tertiary, quaternary structures, and the free sulfhydryl group (−SH) content were measured. The results showed that there was a good correlation between molecular flexibility and emulsifying properties, and the correlation coefficients was 0.920 (P < 0.01) for emulsifying activity and 0.952 (P < 0.01) for emulsion stability. Compared with soy protein isolate, the H 0 of samples at different temperatures first increased and then decreased reaching a maximum at 70 °C, a red shift occurred during the whole given reaction conditions shown by the intrinsic fluorescence spectrum, and the free sulfhydryl content also displayed a marked increase (P < 0.05). At the same time, the particle size gradually became smaller as the degree of grafting increased. The contents of β-turn and random coil increased at the cost of α-helix and β-sheet contents, as evidenced by Fourier transform infrared results. The findings could provide a deep insight into the structure−function relationship of soy protein isolate−glucose conjugates, thus providing theoretical guidance for further research of soy proteins.