Long stroke nanopositioning stages with high natural frequency and compact size are demanded in precision engineering. However, in previous researches, the natural frequency of the long stroke nanopositioning stage is normally below 50 Hz because the actuated force, moving mass, stiffness, motion range, and damping ratio are not considered simultaneously and optimized thereafter. To solve this problem, a long stroke nanopositioning stage driven by the self-damping moving magnet actuator (SMMA) and supported by the flexure guide is integrated and designed in this article. The SMMA consists of two identical tooth-slot structure stators and one moving magnet which is embedded inside the flexure guide. Copper plates that functioned as eddy-current dampers are attached on the tooth surfaces to suppress the resonance peak at the natural frequency. An integrated dynamics model that consists of force, damping coefficient, and stiffness is established. The dimensional parameters of the proposed positioning stage are optimized to improve the system performances based on the developed model. Experimental results show that the natural frequency of the positioning stage reaches up to 71 Hz. The stage can achieve 20 nm positioning resolution within a motion range of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\pm$</tex-math></inline-formula> 5 mm, and the root mean square tracking errors for 1 Hz sinusoidal and triangular commands are below 0.1% of the trajectory amplitudes.