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In this paper, we propose and demonstrate a convenient and flexible approach for preparation large-area of photonic crystals (PhCs) structures on the GaN-based LED chip. The highly-ordered porous anodic alumina (AAO) with pitch of wavelength scale was adopted as a selective dry etching mask for PhCs-pattern transfer. The PhCs with different pore depths were simultaneously formed on the entire surfaces of GaN-based LED chip including ITO, GaN surrounding contacts and the sidewall of the mesa by one-step reactive ion etching (RIE). The light output power improvement of PhCs-based GaN LED was achieved as high as 94% compared to that of the conventional GaN-based LED.