A laminated permanent magnet array eddy current damper (LPMAECD) is proposed to achieve excellent performance for large-scale precision micro-vibration isolation. It improves the damping coefficient by perpendicular magnetized permanent magnet arrays (PMPMA) and laminar arrangement. The PMPMA forms a magnetic field with unilateral characteristics that increase the air gap magnetic flux density and decrease the magnetic flux density near the yoke, thus achieving a high damping coefficient and a low magnetic leakage. Furthermore, the laminar arrangement increases the damping coefficient further and linearly. The theoretical model of LPMAECD is established and validated, and the effect of its geometrical parameters is analyzed. Experimental results show that the damping ratio of the vibration isolation system is raised from 0.12 to 0.32 by LPMAECD, and the peak transmissibility is attenuated by 66%, with the isolation level improved from VC-D to VC-E. It provides an effective method for solving the weak throttling damping of large-scale precision micro-vibration isolation.