Identifying the phase evolution and revealing the chemical bonds of hydrated cements accurately is crucial to regulate the performance of cementitious materials. In this paper, a coupled Raman/BSE-EDS analysis was proposed to determine the chemical bonds of tricalcium silicate hydrates and the interface transition zone (ITZ) between inner C-S-H and anhydrates. The results show that the Raman/BSE-EDS method can accurately identify the chemical bonds of inner C-S-H and inner ITZ regions, which confirms the mixed structure of inner C-S-H and nano calcium hydroxide (CH). The inner ITZ shows a lattice change region with a thickness of 700–1000 nm, which can be attributed to the pre-disassembly process of C3S crystal. The successful application of coupled Raman/BSE-EDS provides new insight into the hydration process and multi-structure features of traditional cementitious materials.