Intestinal microorganisms are essential to the health and production performance of chickens, especially in the research of traditional and organic feeding methods. The intestinal contents of organic and feed chickens were analyzed by 16S rDNA and metagenome technology. The results showed that the microbial diversity of organic chickens was significantly higher than that of the feed chickens, especially the key microorganism such as Enterococcus was more abundant in organic chickens.