Starch, an important carbohydrate with widespread applications in human foods, animal feeds, and many industrial products, is synthesized by plants by the action of a complex system involving many enzymes. The differing activities of these enzymes contribute to variations in starch structure among different plant species, botanical organs, and genetic backgrounds, and thus affect the physicochemical properties and end-use functions of starch. The demand for starches with particular functional properties is increasing, but the ability to produce novel starches is still limited. Starches with specific properties can potentially be produced by biotechnical modification of the starch biosynthetic pathway; however, this requires further understanding of the starch biosynthesis–structure–properties relationships. This review summarizes the state of the art in the understanding of these causal relationships: the roles of the main starch-synthesizing enzymes on starch structure, hierarchical structure of starch, advanced molecular structure characterization methods, and impact of starch structure on some functional properties. A better understanding of these relationships among starch biosynthesis, structure, and properties provides direction for genetic modification and targeted breeding programs to produce starch with desired characteristics.