Human gastrointestinal microbiota plays a major role in the regulation of gastrointestinal immune activity and development of intestinal system. Normal intestinal microflora modulated the physiological functions and affected development of diseases. Infancy is a critical period for the establishment of gastrointestinal microbiota. Intestinal flora in early infancy is dynamic and fragile, and is liable to be influenced by many factors. In this paper, we reviewed the research progress on the influencing factors of infant intestinal microbiota establishment and its relationship with metabolic diseases.