This course introduces the basic structures of matter and its effects on the properties, on the levels of atoms, molecules, clusters and crystals, respectively. We emphasize on the physical origin of the chemical bonds, and how they affect the structure, configuration and the properties of matter. It introduces the origin of symmetry of matter, mainly including the symmetries of molecules and crystals, basic operation of symmetry and the concepts of group. Basic methods for characterization of crystal structure, such as X-ray diffraction, should be mastered (This part of crystal structure is combined with that in the course of Solid State Physics). In more details, it is introduced the atomic structure and atomic orbits, electronic configuration; theory of molecular orbital, valence bond theory, theory of hybridization orbit, chemical bonds, molecular configuration and conformation; structures of carbon and carbon based materials. It also introduces intermolecular interaction, types of interaction force, hydrogen bond, hydrophilic and hydrophobic groups, surface tension and surfactants. During the course, related frontier researches and achievements would be mentioned. The microscopic law inside crystals would be taught in the course of Solid State Physics.