Background: Abatement of odor emissions in poultry production is very important for the quality and safety in poultry industries and benefit to the environment.Methods: This study was conducted to evaluate the effects of the dietary supplementation of different levels soybean oligosaccharides (SBO) in comparison with chlortetracycline (CHL) on major odor-causing compound in excreta and cecal microbiota of broiler chickens. One-day-old broiler chickens were assigned to 6 treatments with 6 replicate pens (10 birds/pen) for the 42-day experiment, including, the negative control (NC) fed a basal diet, the positive control (PC) fed a basal diet with CHL, and the basal diet with SBO at 0.5, 2.0, 3.5, and 5.0 g/kg, respectively. Fresh excreta was sampled for analysis odor compounds by high performance liquid chromatography. Cecum content was collected to analyze the cecal microbiota by 16S rRNA sequencing. Results: The excreta indole concentration of broilers fed 2.0, 3.5 and 5.0 g/kg SBO and CHL diets were significantly decreased (P < 0.01) compared to NC. Excreta skatole concentration (P < 0.001) and pH (P < 0.05) were decreased by SBO and CHL. Formate concentration of birds fed 3.5 and 5.0 g/kg SBO diets were higher than that of birds fed other diets (P < 0.001). The acetate concentration (P = 0.003) were increased in birds fed 3.5 g/kg SBO diet. Deep sequencing 16S rRNA revealed that the composition of the cecal microbial digesta slightly or significantly changed by the supplementation of SBO or CHL. SBO decreased the abundance of Bacteroides, Bilophila, and Escherichia, which were related to indole and skatole concentration of excreta. While CHL had strong tendency to enrich Ruminococcus and reduce Rikenella. Conclusion: These results indicated that supplementation of dietary SBO was beneficial in attenuating the concentration of odor causing compounds and impact the composition cecal microbiota of broilers.