This paper aims at presenting a solution to overcome the problems of small driving force and the evident nonlinear characteristics of the large stroke flexure-based micropositioning stage driven by a voice coil motor (VCM). The push-pull mode of complementary configurations of VCMs on both sides is adopted to improve the magnitude and uniformity of the driving force, and model-free adaptive control (MFAC) is combined to achieve accurate control of the positioning stage. First, the micropositioning stage based on the compound double parallelogram flexure mechanism driven by double VCMs in the push-pull mode is proposed, and its most prominent features are introduced. Then, a comparison of the driving force characteristics of a single VCM and dual VCMs is conducted, and the results are empirically discussed. Subsequently, the static and dynamic modeling of the flexure mechanism was carried out and verified by finite element analysis and experimental tests. After that, the controller for the positioning stage based on MFAC is designed. Finally, three different combinations of different controllers and VCM configuration modes are used to track the triangle wave signals. The experimental results show that compared with the other two combinations, the maximum tracking error and root mean square error of the combination of MFAC and push-pull mode are significantly reduced, which fully proves the effectiveness and feasibility of the method proposed in this paper. At the same time, the reduction of current in the coil confirms the advantages of the push-pull mode.