The interactions between black soybean protein isolate (B-SPI) and cyanidin 3-O-glucoside (C3G), anthocyanin extracted from black soybean coat was investigated under neutral conditions. The fluorescence spectra showed that C3G had fluorescence quenching effects on B-SPI. Thermodynamic parameters showed that ∆G < 0, which demonstrated that the binding was a spontaneous reaction. Since ΔH > 0 and ΔS > 0, the interactions between C3G and B-SPI was mainly hydrophobic interactions. Fourier infrared spectroscopy results suggested that the contents of α-helix and β-sheet structure showed an increasing trend, whereas the β-angle content displayed a decreasing trend. The degradation of C3G followed first-order kinetics at 85 °C and 100 °C. After the interactions with B-SPI, the degradation rate constant was decreased and the half-life of C3G was prolonged from 70.25 ± 0.90 min to 175.64 ± 38.04 min at 85 °C, from 62.68 ± 1.1 min to 72.51 ± 2.5 min at 100 °C (p < 0.05). The results indicated that the interactions of B-SPI and C3G improved the thermal stability of C3G under heating conditions.