The cecum of poultry harbors a complex and dynamic microbial community which plays important roles in preventing pathogen colonization, detoxifying harmful substances, nutrient processing, and harvesting of the ingestion. Understanding and optimizing microbial communities could help improve agricultural productivity. In this study, we analyzed the composition and function of cecal microbiota of Wenchang chicken (a native breed of Bantam) before and after fattening, using high throughput sequencing technology. High-throughput sequencing of the 16S rRNA genes V3-V4 hypervariable regions was used to characterize and compare the cecal microbiota of Wenchang chicken before fattening (free-range in hill) and after fattening (cage raising). Sixteen phyla were shared by the 20 samples. Firmicutes and Bacteroidetes were the top two abundant phyla being 80% of the total microbiota. Samples of chickens prior to fattening were more dispersed than those after fattening. Twenty four microbes could be considered as biomarkers and 3 phyla revealed differences by variance analysis which could distinguish the two groups. Cecal microbiota in the before fattening group had higher abundance of functions involved in digestive system and biosynthesis of other secondary metabolites. The composition and function of cecal microbiota in Wenchang chicken before and after fattening under the two feeding modes, free range in hillside and cage raising, were found to be different. These results can be attributed to the differences in feeding modes and growth stages. In-depth study on the functions and interactions of intestinal microbiota can help us in developing strategies for raising Wenchang chickens and provide valuable information for the study of microbiota in the chicken gut.