Piezodriven flexure-based motion stages, with a large workspace and high positioning precision, are really attractive for the realization of high-performance atomic force microscope (AFM) scanning. In this paper, a modified lever displacement amplifier is proposed for the mechanism design of a novel compliant two-degree-of-freedom (2-DOF) nanopositioning stage, which can be selected to drive in dual modes. Besides, the modified double four-bar parallelogram, P (P denotes prismatic) joints are adopted in designing the flexure limbs. The established models for the mechanical performance evaluation of the stage, in terms of kinetostatics, dynamics, and workspace, are validated by the finite-element analysis. After a series of dimension optimizations carried out through the particle swarm optimization algorithm, a novel active disturbance rejection controller, including the nonlinearity tracking differentiator, the extended state observer, and the nonlinear state error feedback, is proposed to automatically estimate and suppress plant uncertainties arising from the hysteresis nonlinearity, creep effect, sensor noises, and unknown disturbances. The simulation and prototype test results indicate that the first natural frequency of the proposed stage is approximated to be 831 Hz, the amplification ratio in two axes is about 4.2, and the workspace is 119.7 μm × 121.4 μm, while the cross coupling between the two axes is kept within 2%. All the results prove that the developed stage possesses a good property for high-performance AFM scanning.