Flexure-based scanning stages driven by piezoelectric (PZT) actuator with large stroke, nanoscale precision, and high bandwidth are quite appealing for developing an advanced multiphoton polymerization 3-D nanolithography system. The motivation of this article is to develop a nanopositioning system, which can simultaneously achieve large stroke, high bandwidth, and nanoscale precision to ensure its machining size, efficiency, and accuracy without traditional step-by-step splicing operations. First, anXYnanopositioning stage with millimeter-scale workspace and nanoscale positioning accuracy is designed. Besides, the natural frequency modeling of the nanopositioning stage is conducted by resorting to compliance analysis based on the matrix method, which is validated by a finite-element analysis (FEA). Moreover, linear active disturbance rejection controller (LADRC) is demonstrated that it can be equivalent to a PID controller filtered using a second-order low-pass filter, which theoretically verifies the effectiveness of controlling the nanopositioning stage. In order to complete LADRC’s successful implementation for nanopositioning stage, a novel quantitative one-parameter-tuning method of LADRC is proposed. Finally, a series of trajectory tracking experiments has been carried out to verify the effectiveness and superiority of the proposed nanopositioning stage. The experimental results verify that the large-stroke compliant nanopositioning system has the capability to achieve millimeter stroke, which has reached 1.035 mm$\times \,\,1.035$mm, while the average tracking error is kept within ±100 nm, and the closed-loop bandwidth is achieved up to 32 Hz.Note to Practitioners—With the purpose to effectively improve the performance in terms of stroke, speed, and accuracy for the piezoelectric (PZT)-actuated scanning system, a completely decoupled nanopositioning stage with millimeter-scale travel range is developed and linear active disturbance rejection controller (LADRC) strategy with a novel quantitative one-parameter-tuning method of strategy is proposed. Experimental results indicate that the compliant nanopositioning system has the capability to achieve millimeter stroke, which has reached 1.035 mm$\times \,\,1.035$mm, while the average tracking error of dynamic tracking control of the nanopositioning stage is kept within ±100 nm, and the closed-loop bandwidth is achieved up to 32 Hz. Therefore, the developed nanopositioning system has satisfactory performance for fulfilling advanced large-size multiphoton polymerization 3-D nanolithography task without step-by-step splicing operations. In summary, the potential applications of the proposed large-stroke nanopositioning strategy will be promising.