Human milk oligosaccharides (HMOs) are a unique class of non-digestible carbohydrates present in the mother milk, which play a key role in the development of infant gut microbiota, epithelial barrier and immune function. The deficiency of HMOs in the bovine milk-based infant formula has been widely recognized as a major culprit for the much higher incidence of immune disorders of formula-fed infants. This report was to give an up-to-date review on the structure characteristics of HMOs and the possible mechanisms, and strategies for their cellular uptake, and metabolism by the gut bacteria and the associated effects on the infant gut microbiome, and immune function. Most previous studies have been carried out in animals or in vitro model systems on the utilization strategies for HMOs in infant bacteria and their roles in infant microbiome, and gut immune function. A few HMO molecules have been synthesized artificially and applied in infant formulas. •HMOs have diverse structures mostly composed of five sugar residues with a DP of 3–32.•HMOs play important roles in development of infant microbiome and immune function.•HMOs are degraded extra-/intra-cellularly and utilized selectively by infant gut bacteria.•A few HMOs have been synthesized and applied in infant formula milk.•Much more effort is needed to understand the function and mechanism of HMOs in infant health.