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 magnetic levitation zero-rigidity vibration isolator. A magnetic levitation thrust bearing is used for bearing between a sleeve of a vibration isolator body and an air floatation plate, an air floatation surface is used for lubricating and supporting between the air floatation plate and a lower mounting 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 magnetic levitation zero-rigidity vibration isolator has the advantages of zero three-dimensional rigidity, high positioning precision, decoupling of degree of freedom of linear motion and degree of freedom of angular motion and the like, and is capable of effectively achieving high-performance vibration isolation in ultra-precise measuring instruments and processing equipment, particularly in step-scan lithography machines.