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Light-induced rapid annealing (LIRA) is a widely used method to modify the morphology and crystallinity of noble metal nanoparticles, and the nanoparticles generally evolve into nanospheres. It is rather challenging to form faceted Au nanocrystals on a substrate using LIRA. Here the formation of spatially ordered Au nanocrystals using a continuous wave infrared laser is reported, assisted by a metamaterial perfect absorber. Faceted Au nanocrystals in truncated-octahedral or multi-twinned geometries can be obtained. The evolution of morphology and crystallinity of the Au nanoparticles during laser annealing is also revealed, where the crystal grain growth and the surface melting are shown to play key roles in nanocrystal formation. The evolution of morphology also gives the freedom of tuning the absorption spectrum of the metamaterial absorber. These findings provide a novel way for tailoring the morphology and crystallinity of metallic nanoparticles and may pave the way to fabricate refined nano-devices in many potential applications for optics, electronics, catalysis, surface-chemistry and biology.