Gut micriobiota have important roles in the immune, nutrition, and physiology of animals. To study the cause of gut microbiota change in black-necked cranes, we collected 9fresh Black-necked cranes’ fecal samples from Dashanbao Reserve. High throughput Illumina sequencing technology was used to analyze the microbial community structure of the collected samples for the V4 region of the 16S rRNA gene. Proteobacteria (44.14%) followed by Firmicutes (17.95%) and Bacteroidetes (9.97%) were the core dominant groups, and all of them play a role in the degradation of cellulose in Black-necked cranes. Bacteroidetes and Firmicutes contain glycan degrading enzymes, play a vital role in polysaccharide fermentation, and could help the host obtain more energy and materials. Higher Proteobacteria were unusual in birds. To explain this phenomenon, we analyzed the genus abundance of Proteobacteria in detail, found that Psychrobacter has the highest abundance and can grow at sub-zero temperatures. Through comparison, it was show that there were certain differences in the abundance of gut microbiota in different period The significance of this study was to provide a reference for understanding the function of intestinal microbiota and factors of gut microbiota structure change of Black-necked cranes and other migratory waterbirds.