Partial denitrification/anammox (PD/A) has been recently applied to co-treat domestic wastewater and nitrate-containing anammox effluent. However, studies regarding its performance without external organic supplement, spatial characteristics within sludge aggregates, and chronological changes of active microorganisms along PD/A cycle have rarely been reported. Herein, one-stage PD/A unit extremely and simultaneously polished anammox-pretreated reject water (NH4+-N: 65.4 ± 5.7 mg/L, COD: 199.7 ± 23.2 mg/L) and domestic wastewater (NO3−-N: 81.6 ± 7.8 mg/L, TN: 85.8 ± 8.9 mg/L, COD: 338.2 ± 29.0 mg/L) to 4.5 ± 2.1 mg/L without external organic carbon supply. Protective “granules-in-granule” aggregates with densely clustered anammox bacteria embedded in homogeneous denitrifying Thauera prevailed in PD/A system, surviving disadvantages from complex wastewater. Uronic acids and β-sheet proteins in outer extracellular matrix facilitated granulation and pollutants adsorption, while tryptophan- and aromatic-like proteins with tighter secondary structure in inner extracellular matrix maintained granular robustness. Importantly, succession of active microorganisms along the PD/A cycle was revealed by transcript-level analysis for the first time. In PD-period, stimulated Thauera contributed to rapid nitrite accumulation. In subsequent anammox-period, Ca.Brocadia was activated to conduct advanced nitrogen removal, which accompanied the timely nitrate-to-nitrite reduction by Thauera and Ca.Competibacter. Elusimicrobia was active throughout the PD/A cycle, which is conducive to eliminate the dependence of PD process on external carbon source by decomposing complex organics in actual wastewater. Protective granular structure, orderly activation and harmonious cooperation of functional consortia facilitated practical nitrogen removal rate of 0.6 ± 0.1 kg-N/m3/d under anoxic condition, which sheds light on engineering application of anammox technology.