In this paper, We present the design, control and implementation of a novel, compact and three degree-offreedom (DOF) precise flexure-mechanism electromagnetic-actuating positioning system with submocrometer-scale precise positioning capability and millimeter-level large travel range. The design of the positioner utilizes the monolithic parallel flexure mechanism with the built-in electromagnetic actuators and the eddy-current sensors to achieve the 3-DOF motion. The positioner presented herein shows the planar travel range of 1mm×1mm with a position resolution of ±300 nm. To let the compact system be more robust and stable in positioning, we propose an adaptive sliding-mode controller. We will demonstrate the satisfactory performance of the positioning system, including stiffness and precision, with theoretical analysis and experimental results.