Recent development of molecular biology and high-throughput sequencing (next generation sequencing, NGS) technologies make our deeper understanding possible for the giant panda gut flora, both in the community structure and function. Studies have found that the giant panda’s intestinal flora plays an important role in the host immunity, digestion and metabolism, which could be affected by many factors including the digestive tract structure, diet, season and age. This article reviews the progress of intestinal bacterial community structure and biological characteristics of the giant panda, and discusses the future research directions.