Intestinal microecology is an important and complex biological system essential to human health. Intestinal microecology and the liver are closely related in anatomical structure and function. Infantile cholestatic liver disease lead to abnormal bile secretion, abnormal excretion, and reduced bile release into the intestinal tract. As a result, the intestinal mucosa barrier is damaged and intestinal microecology changes; at the same time, pathogenic bacteria and endotoxin translocation cause liver injury and aggravate cholestasis. Therefore, a close relationship of intestinal microecology with infantile cholestatic liver disease can be found. In this article, the relationship of intestinal microecology with the development and progression of infantile cholestatic liver disease is illustrated and it is concluded that probiotics should be given as a supplement when infantile cholestatic liver disease occurs, because it promotes bile secretion, blocks intestinal inflammatory reactions, and improves prognosis of the disease. It is recommended to provide microecological agents routinely as a method to prevent and treat infantile cholestatic liver disease.