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When ultra-thin graphite intercalation compounds (GICs) are deposited on the SiO2/Si substrate, it is found that their colors are dependent on the thickness of GIC flakes. The sample colors of ultrathin GIC flakes can no longer provide qualitative information on the stage index. Here, multi-wavelength Raman spectroscopy is thus applied to study the doping inhomogeneity and staging of ultra-thin GICs by FeCl3 intercalation. The G band intensity of stage-1 GIC flakes is strongly enhanced by 532-nm laser excitation, while that of stage-2 and stage-3 flakes exhibits strong intensity enhancement for 785-nm laser excitation. The near-infrared lasers are suggested to probe the doping inhomogeneity and staging of ultra-thin GIC flakes.