•Partial nitrification granular sludge was successfully cultivated in a SBR.•The effluent NH4+-N/NO2−-N ratio was about 1:1 with NAR at 87.8%.•MLSS and SVI30 of SBR were 14.6 g/L and 25.0 mL/g, respectively.•Nitrosomonas affiliated to the AOB was the predominant group. Partial nitrification granular sludge was successfully cultivated in a sequencing batch reactor as a pretreatment for anaerobic ammonium oxidation (Anammox) through shortening settling time. After 250-days operation, the effluent NH4+-N and NO2−-N concentrations were average at 277.5 and 280.5 mg/L with nitrite accumulation rate of 87.8%, making it as an ideal influent for Anammox. Simultaneous free ammonia (FA) and free nitrous acid (FNA) played major inhibitory roles on the activity of nitrite oxidizing bacteria (NOB). The MLSS and SVI30 of partial nitrification reactor were 14.6 g/L and 25.0 mL/g, respectively. Polysaccharide (PS) and protein (PN) amounts in extracellular polymeric substances (EPS) from granular sludge were about 1.3 and 2.8 times higher than from seed sludge. High-throughput pyrosequencing results indicated that Nitrosomonas affiliated to the ammonia oxidizing bacteria (AOB) was the predominant group with a proportion of 24.1% in the partial nitrification system.