Starch and glycogen, as the primary reservoirs of energy in most living organisms, play a pivotal role in regulating metabolic processes and maintaining health. The molecular structure of these polysaccharides is a major determinant of their impact on the metabolism and overall health of the organism. This review discusses the effects of the molecular structures of starch and glycogen on human health, and provides an analysis of their structural levels, extraction methods, structural characterization techniques, mathematical models of structure, and the implications of their molecular structures for health. It offers insights into the similarities and differences between the molecular structures of starch and glycogen, and examines the role these structures play in pathological conditions. Furthermore, it presents a perspective on how the relationship between the fine structure of these biopolymers and health could lead to new findings in the biosynthesis-structure-property relations for these polymers and their impact on human well-being.