Human gastrointestinal is a diversified and live microecological system, and a body site of scientific interest. Intestinal tract comprises 100 trillion and nearly 1 000 to 1 150 bacterial phylotypes that interact and influence the health of the human host. The influences could be positive or with potential threats. In this paper, the relationship between gastrointestinal microbiota and diseases, the effect of probiotics on human health, and the new approach of researching on the gastrointestinal microbiota are reviewed to provide references for domestic researchers, and to raise the awareness of general public regarding gastrointestinal health