Nanopositioning systems are very popular and playing an increasingly vital role in micro and nano-scale positioning industry due to their unique ability to achieve high-precision and high-speed operation. However, hysteresis, commonly existing in piezoelectric actuators, degrades the precision seriously. Uncertain dynamics and sensor noises also greatly affect the accuracy. To address those challenges, a variable bandwidth active disturbance rejection control (VBADRC) is proposed and realized on a nanopositioning stage. All undesired issues are estimated by a time-varying extended state observer (TESO), and cancelled out by a variable bandwidth controller. Convergence of the TESO, advantages of a TESO over a linear extended state observer (LESO), and the closed-loop stability of the VBADRC are proven theoretically. Improvements of the VBADRC versus the linear active disturbance rejection control (LADRC) are validated by simulations and experiments. Both numerical and experimental results demonstrate that the VBADRC is not only able to provide the same disturbance estimation ability as the LADRC, but also more powerful in noise attenuation and reference tracking.