Different synthetic wastewaters are used to analyze the effect of organic carbon on the nitrogen removal and microbial community in the completely autotrophic nitrogen removal process. Results show that the nitrogen removal performance is improved by control of DO at a reasonable C/N ratio. The NH +4-N is removed in several ways. When the influent without any organic carbon, the most of ammonium is removed in nitrification-ANAMMOX metabolic pathway; the contribution of nitrification-ANAMMOX decreases, while the conventional nitrification-denitrification process enhanced with the addition of organic carbon. PCR-DGGE and statistical analyses show that the microbial diversity in SBBR reactor fed with organic wastewater is more abundant than it fed with inorganic wastewater，and this exhibits obvious in the biofilm, which also indicate that it helps to format the aerobic-anaerobic microenvironment，so nitrogen can be removed in different ways in one reactor.