A spontaneous development of full-scale anaerobic ammonium oxidation (anammox) process was seldom reported, and its operational parameters could supply references in actual applications. This engineered case indicated that anammox process was suitable for treating relatively high-strength ammonium and organics wastewater due to niche differentiation of biofilm. Results of isotope labelling showed that anammox contributed approximately 40% to N-loss in aerobic unit, but this value increased to 78.3% in anoxic tank. Mass balance showed that N-removal via anammox and denitrification pathways were 38.1 and 23.9 g m d, and anammox rate was 1.6 times higher than denitrifiaction. The wild-type anammox granules had a high purity, with anammox accounting for 92.2%. Candidatus Brocadia was the predominant species. Mixing sludge had a higher oxygen tolerance compared with granules, although the latter had a higher anammox activity under anaerobic conditions. Moreover, physicochemical precipitation on the surface of granules may be related to granulation mechanism.