As a natural low-calorie sweetener, Mogroside V (Mog-V) has gradually become one of the alternatives to sucrose with superior health attributes. However, Mog-V will bring unpleasant aftertastes when exceeding a threshold concentration. To investigate the possibility of soy protein isolates (SPIs), namely β-conglycinin (7S), and glycinin (11S) as flavor-improving agents of Mog-V, the binding mechanism between Mog-V and SPIs was explored through multi-spectroscopy, particle size, zeta potential, and computational simulation. The results of the multi-spectroscopic experiments indicated that Mog-V enhanced the fluorescence of 7S/11S protein in a static mode. The binding affinity of 7S-Mog-V was greater compared with 11S-Mog-V. Particle size and zeta potential analysis revealed that the interaction could promote aggregation of 7S/11S protein with different stability. Furthermore, computational simulations further confirmed that Mog-V could interact with the 7S/11S protein in different ways. This research provides a theoretical foundation for the development and application of SPI to improve the flavor of Mog-V, opening a new avenue for further expanding the market demand for Mog-V.