Colloidal crystals composed of micro- or nano- colloids have been investigated in various fields such as photonics due to their unique optical properties. Binary colloidal crystals have an outstanding potential for fine-tuning material properties by changing the components, concentration, or size of colloids. Because of their tunable optical, electrical, magnetic, and mechanical properties, those materials attracted great attention. However, it has been hard to elucidate internal structures without fluorescent labelling or cross-sectioning. Here, we demonstrate the structural analysis of not only unary but also binary colloidal crystals using scanning transmission x-ray microscopy and compare the results with colloidal structures and optical properties observed by optical microscopy. Based on the comparison of images obtained by these two methods, the domains of colloidal crystals consisting of different structures and colours were directly identified without any additional sample preparation. Therefore, it was possible to investigate the structural colours of local domains of unary and binary colloidal crystals such as the face centred cubic (FCC) structure with different orientations, that is FCC (111) and FCC (001), and hexagonal close-packed structure, HCP (0001).