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We propose a fast numerical method to evaluate total quality factor of photonic-crystal-slab-based donor-like micro- cavity. Substantive computations and time are saved by two dimensional finite-difference time-domain (2D-FDTD) and 3d plane-wave expansion (PWE) technique instead of full 3D-FDTD. In-plane quality factor and mode of cavity are calculated simultaneously by 2D-FDTD technique with 3d-to-2d effective index method (EIM). The effective index is computed based on the effective index perturbation (EIP) method , which assures the coherence of the cavity mode from 3D-FDTD and 2D-FDTD. Out-plane quality factor, scattering loss in direction perpendicular to the plane, is estimated by near-field scattering method [2, 3] based on the calculated 2d cavity mode and an approximation that electromagnetic field profile in out-plane direction is as same as mode of 2d infinite slab. The time consume for each cavity is less than an hour. By repeating the cavity geometry tuning in the silicon triangle silicon photonic crystal slab micro-cavity reported by Yoshihiro and Takashi [4, 5], good match of quality factors of our technique and 3D-FDTD has been proved. Finally, optimized quality factor of photonic crystal slab with low contrast cladding are reported.