To explore better methods of natural protein modification for black soybean, comparisons among the effects of different modified methods on structural changes of the modified products of black soybean protein isolate (BSPI) were carried out in this study. The modified products used in this study included enzymatic crossing-link black soybean protein isolate (ECBSPI), wet heating treatment glycosylation black soybean protein isolate (WHTGBSPI) and especially enzymatic glycosylation black soybean protein isolate catalyzed by transglutaminase (EGBSPI). The effects of the modification methods on structural changes were analyzed by SDS-polyacrylamide gel electrophoresis (SDS-PAGE), amino acid content and circular dichroism (CD) analysis. Moreover, the processing properties changes caused by structural changes of BSPI were detected by thermogravimetric analysis, particle size analysis, zeta-potential, surface hydrophobicity, solubility, emulsification, gelation, and rheological properties. The results show that the modified BSPI products were protein polymers, and among them, EGBSP and WHTGBSPI are covalently bonded glycation products. Products modified by Maillard reactions and transglutaminase (TG) display partly destroyed α-helix and β-sheet structures that form more open secondary BSPI structures. For ECBSPI, the proportion of irregular crimp structure reduces to form a high order secondary structure. All the modified products form fine aggregations in dispersion, except WHTGBSPI has most negative zeta-potential and least molecular stability due to the hydrophobic amino acids embedded in the protein molecules. The zeta-potentials of BSPI, ECBSPI, WHTGBSPI and EGBSPI are respectively −21.5, −23.8, −18.1 and −20.2 mV. The surface hydrophobicity of EGBSPI (5.07 ± 0.07) and WHTGBSPI (7.02 ± 0.05) decrease, while the surface hydrophobicity of ECBSPI (19.5 ± 0.06) increases. The solubility and rheological properties of EGBSPI, ECBSPI and WHTGBSPI after modification are all better than those of BSPI, especially EGBSPI. Emulsification of EGBSPI and WHTGBSPI increase (by 24.5% and 12.2%, respectively) while ECBSPI decrease (by 17.0), and there is similar emulsion stability trend. Moreover, the properties of ECBSPI increase except cohesiveness compared to BSPI. In conclusion, as a safe and efficient method for natural protein modification, enzymatic glycosylation catalyzed by TG has great potential in improving food processing characteristics.