Different synthetic wastewaters were used in the batch tests to analyze the intermediate products and the nitrogen balance, and to study the mechanism of ammonium removal in the completely autotrophic nitrogen removal in one reactor process with the sludge cultured in the SBBR completely autotrophic nitrogen removal system. The results showed that 62% of ammonium was converted to such nitrogen compounds as NO2-, NO3-, NH2 OH, N2H4, NO, NO2, N2O and N2 without addition of organic carbon, and N2 took up 90.07%. The ammonium in the completely autotrophic nitrogen removal in one reactor system was removed in many ways. 4.5% of ammonium was removed in the physical-chemical way. 3.73% of ammonium was converted by the conventional nitrification-denitrification process. The quantity of ammonium removed by the completely autotrophic nitrogen removal in one reactor process was 53.77%, which is the largest, and the completely autotrophic nitrogen removal in one reactor process could be realized in two different metabolic pathways. But the effluent ammonium in the anoxic reactor, where enough NO2 present were present, was equal to the blank system, and no ammonium was converted to such nitrogen compounds as NO2- and N2 by Nitrosomonas eutropha using NO2 as electron acceptor, which maybe caused by lack of the function bacteria.