Abstract Piezoelectric-driven flexure micro/nanopositioning stages often exhibit a low-damping resonance mode, which can easily excite mechanical resonance during high-speed movement, and significantly impact the control system's stability, control bandwidth, and trajectory tracking accuracy. To mitigate the reliance on the precise modeling of stage dynamics inherent in current resonant controllers, an adaptive control method based on a back propagation (BP) neural network was designed to suppress resonance in real-time. First, a piezoelectric-driven flexure micro/nanopositioning stage system was constructed. Next, a feedback controller similar to a notch filter was designed, with bilinear transformation applied based on the system's inherent parameters to determine the initial values. Finally, the designed adaptive control method was tested through trajectory tracking experiments using a triangular wave signal. The experimental results showed that, when tracking the triangular wave signal, the maximum tracking error was reduced by 72.66% compared to proportional-integral (PI) control alone and by 68.66% compared to proportional integral control combined with a traditional notch filter. The tracking results demonstrate a significant improvement in the stage's stability and tracking accuracy.