Two-dimension photonic crystal slab micro-cavity exist radiation loss in the vertical direction, which decreases the quality factor and restricts its application. According to the Fourier analysis of photonic crystal slab micro-cavity loss, this paper adopts the method of modulating cavity mode profile, which reduces the distribution of wave vector in radiation lead area, decreases the cavity loss, and realizes the optimization of cavity quality factor. Facing to the structure design of two-dimension photonic crystal slab L3 micro-cavity, this paper gives a numerical simulation to photonic crystal slab L3 micro-cavity. The simulation results show a great improvement of cavity quality factor, and validate effectiveness of the optimization method for photonic crystal micro-cavity quality factor in this paper.