In this study, the oral saliva samples of 6 captive giant pandas were sequenced by high-throughput sequencing technology with an aim to analyze the oral microflora diversity, structure, potential pathogenic bacteria and the differences between the two groups of captive giant pandas in different ages. The results showed that the bacteria in the mouth of giant pandas were mainly Proteobacteria (70.4%) and Cyanobacteria(13.4%) at the phylum classification level. At the level of genus classification, Actinobacillus (10.5%), Lautropia(5.4%), Pseudomonas(3.9%) and Moraxella(3.8%) were the main species. The diversity and richness of oral flora of sub-adult giant pandas were higher than those of elderly giant pandas with no significant difference. The β diversity analysis showed that there was no significant difference in oral flora structure between the two groups. The LEfSe analysis revealed that the different bacteria of the two groups were Niveispirillum, Azospirillum and Rhizobium in the sub-adult group, while Arenimonas and Capnocytophaga were found in the senile group, but their abundance were not high. At the same time, we found Streptococcus, Actinomyces, Porphyromonas, Staphylococcus and other pathogenic bacteria in the mouth of captive giant pandas, among which the abundance of caries-related bacteria were higher, which might be related to the more carbohydrate intake of captive pandas.