The invention belongs to the technical field of precision vibration isolation and relates to a double-layer orthogonal air floatation decoupling and flexible membrane angular decoupling electromagnetic damping vibration isolator. Air floatation surfaces are used for lubricating and supporting between a sleeve of a vibration isolator body and an air floatation plate as well as between the air floatation plate and a lower mounting plate, an electromagnetic damper is used for attenuating vibration energy between the sleeve and the air floatation plate, degree of freedom of horizontal linear motion between an upper mounting plate and the lower mounting plate is decoupled by double-layer orthogonal air floatation guide rails, degree of freedom of angular motion between the upper mounting plate and the lower mounting plate is decoupled by a flexible membrane, and voice coil motors, displacement sensors, limit switches, a controller and a drive form a position closed-loop feedback control system so as to precisely control the relative position of the upper mounting plate and the lower mounting plate. The electromagnetic damping vibration isolator vibration isolator has the advantages of zero three-dimensional rigidity, high positioning precision and decoupling of degree of freedom of linear motion and degree of freedom of angular motion, and is capable of effectively achieving high-performance vibration isolation in ultra-precise measuring instruments and processing equipment, particularly in step-scan lithography machines.