In this paper, the complex structure of CuInGaSe (CIGS), which is fabricated by a two-step progress (the deposition step and the salinization) or co-evaporation method, is analyzed in detail by several methods. Rutherford backscattering spectroscopy (RBS) shows unique advantage for investigating CIGS multi-layer. For the two-step CIGS thin films, both Ga and In atoms reveal a gradient distribution. Such a distribution that Ga atoms are more likely to be localized in a deeper layer of surface than in a shallow layer of surface, has no relation with the Mo layer. RBS and Auger electron spectroscopy (AES) prove that there appears diffusion in the interfaces of multi-layers, especially the interfaces of CdS and CIGS, Mo and CIGS. X-ray fluorescence (XRF) indicates that CIGS thin film presents the highest efficiency when the content ratio of In and Ga atoms is 0.7:0.3. Structural investigation by X-ray diffraction reveals the improved crystalline quality after annealing.