Abstract: After low-permeability reservoirs enter the middle-high water-cut stage, waterflooding performance declines markedly due to low matrix permeability, well-developed fractures, and water channeling. To elucidate the deep-profile control mechanism of nanosphere flooding and optimize injection parameters, a dynamic profile-control experimental method for a matrix-fracture parallel system was established. Combined with nuclear magnetic resonance measurements and correlation analysis, profile-control experiments were conducted under different nanosphere sizes, injection rates, and mass fractions, and the plugging efficiency, oil recovery, and variations in fracture conductivity were systematically evaluated. The results indicate that nanospheres preferentially migrate into plug fractures and dominant flow channels during injection, thereby enabling matrix-fracture synergistic mobilization and deep profile control. The 50 nm nanospheres exhibit superior long-term plugging stability and fracture conductivity control compared with the 100 nm nanospheres. At an injection rate of 0.03 mL/min and a mass fraction of 0.10%, the 50 nm nanospheres achieve the highest plugging efficiency (22.94%) and the most pronounced recovery improvement, accompanied by a more balanced fluid distribution between the matrix and fractures. These findings provide a basis for optimizing profile-control parameters and achieving stable production in low-permeability reservoirs at the middle-high water-cut stage.