Early nutrition has an enormous influence on a child's physiological function, immune system maturation, and cognitive development. Human breast milk (HBM) is recognized as the gold standard for human infant nutrition. According to a WHO report, breastfeeding is considered as an unequaled way of providing ideal food to the infant, which is required for his healthy growth and development. HBM contains various macronutrients (carbohydrates, proteins, lipids, and vitamins) as well as numerous bioactive compounds and interactive elements (growth factors, hormones, cytokines, chemokines, and antimicrobial compounds. The aim of this review is to summarize and discuss the current knowledge about metabolites, which are the least understood components of HBM, and their potential role in infant development. We focus on small metabolites (<1500 Da) and characterize the chemical structure and biological function of polar metabolites such as human milk oligosaccharides, nonprotein molecules containing nitrogen (creatine, amino acids, nucleotides, polyamines), and nonpolar lipids. We believe that this manuscript will provide a comprehensive insight into a HBM metabolite composition, chemical structure, and their role in a child's early life nutrition.