Due to the excellent advantages of high speed, high precision, and driving force, piezoelectric actuators nanopositioning systems have been widely used in various micro/nanomachining fields. However, the inherent resonance dynamic of the nanopositioning system generated by the flexure-hinge greatly deteriorates the positioning performance and limits the closed-loop bandwidth. Even worse, the notch filter for eliminating the effect of resonance does not work due to the varying resonant frequency resulting from the external disturbance or mass load. To this end, an adaptive notch filter for piezo-actuated nanopositioning system via position and online estimate dual-mode (POEDM) has been proposed in this paper, which can estimate the varying resonant frequency in real-time and suppress the resonance to improve the closed-loop bandwidth. First, a novel variable forgetting factor recursive least squares (VFF-RLS) algorithm for estimating resonant frequency online is presented, which is robust to the noise and provides the performances of both fast tracking and stability. Then, a POEDM method is proposed to achieve the online identification of the resonant frequency in the presence of noise and disturbance. Finally, a series of validation simulations are carried out, and the results indicate that, the frequency of input signal and the bandwidth have been achieved up to 12.5% and 87.5% of the first resonant frequency, respectively.