There are no reports involved the intestinal microbiota from Chinese infants with short bowel syndrome (SBS) under different clinical status. Alterations in the microbiota are closely correlated with the bile acids and short chain fatty acids metabolism as well as the intestinal immunity. A relatively comprehensive profile composed of microbial structure, microbial metabolism products and immune biomarkers in SBS infants may facilitate a better therapy strategy to complications occurred in SBS children.