A nanometer precision six-DOF magnetic suspension micro-stage and the application thereof are provided which are mainly used in semiconductor photolithography devices. The micro-stage includes a cross support and four two-DOF actuators. Each 2-DOF actuator comprises a vertically polarized permanent magnet, a horizontal force coil and a vertical force coil; the permanent magnet being mounted on an end of the cross support, the horizontal force coil and the vertical force coil being arranged on a side of and below the permanent magnet respectively and being spaced apart from the permanent magnet; the cross support and four vertically polarized permanent magnets constitute a mover of the micro-stage; the horizontal force coil and the vertical force coil being fixed by a coil framework respectively and constituting a stator of the micro-stage; and the stator being mounted on a base of the micro-stage. A dual-wafer table positioning system of a photolithography machine may be constructed by two said micro-stages in combination with a two-DOF large stroke linear motor. The present invention features simple structure, large driving force, small mass and absence of cable disturbance, and is possible to realize high precision, high acceleration six-DOF micro-motion.