The existing micro-motion stage based on flexure hinge can hardly meet the requirements of a high-precision stage with large stroke and variable operating conditions (especially variable frequency operation). In this paper, a flexible hinge micro-motion stage with adjustable stiffness is presented. A wide range of stiffness and frequency adjustments are realized by changing the length of the flexure hinge through the movement of the support. However, the change on the stiffness of the flexure hinge is non-linear when is in large deformation. It is difficult to use the traditional PID algorithm to control such nonlinear system without the complete mathematical model, and much more complicated control strategies are required to deal with the condition of large deformation of the flexure hinge. In this paper, the active disturbance rejection control (ADRC) strategy is adopted to solve the above non-linear control problem without relying on the complete system model. A novel model-compensated ADRC based on the dynamic characteristics is proposed to further improve the performance of the micro-motion stage. Experiments show that the ADRC with model compensation (MADRC) can achieve high positioning and tracking precision faster than the conventional ADRC. The presented micro-motion stage based on stiffness-adjustable flexure hinges and MADRC design is capable to meet the industrial application requirements of large stroke or variable working conditions.