This paper presents a novel design and control strategies for a parallel two degrees-of-freedom (DOF) flexure-based micropositioning stage for large-range manipulation applications. The motion-guiding beam utilizes a compound hybrid compliant prismatic joint (CHCPJ) composed of corrugated and leaf flexures, ensuring increased compliance in primary directions and optimal stress distribution with minimal longitudinal length. Additionally, a four-beam parallelogram compliant prismatic joint (4BPCPJ) is used to improve the motion decoupling performance by increasing the off-axis to primary stiffness ratio. The mechanism’s output compliance and dynamic characteristics are analyzed using the compliance matrix method and Lagrange approach, respectively. The accuracy of the analysis is verified through finite element analysis (FEA) simulation. In order to examine the mechanism performance, a laser interferometer-based experimental setup is established. In addition, a linear active disturbance rejection control (LADRC) is developed to enhance the motion quality. Experimental results illustrate that the mechanism has the capability to provide a range of 2.5 mm and a resolution of 0.4 μm in both the X and Y axes. Furthermore, the developed stage has improved trajectory tracking and disturbance rejection capabilities.