To achieve efficient biological nutrients removal at low temperature, a modified sequencing batch reactor (SBR) was developed at 10 °C by extending sludge retention time (SRT), shortening aerobic stage and compensating anoxic stage. The average removal rates of ammonium (NH-N), total nitrogen (TN) and total phosphorus (TP) were 98.82%, 94.12% and 96.04%, respectively. Variation of carbon source in a typical cycle demonstrated the maximum synthesis of poly-β-hydroxybutyrate (PHB) (60 mg/L) occurred after feast period. Furthermore, the TP in sludge reached 50.4 mg/g mixed liquor suspended solids (MLSS) (78.4% was inorganic phosphorus and 21.6% was organic phosphorus) after 120 days of operation, indicating an excellent P-accumulating capacity was achieved in this system. Ammonia oxidizing bacteria (AOB) activity inhibition test verified both AOB and ammonia oxidizing archaea (AOA) were involved in ammonia-oxidizing process and the latter accounted for 17%-19%. Metagenomic-based taxonomy revealed the dominant genera were Candidatus Accumulibacter (12.18%), Dechloromonas (7.54%), Haliangium (6.69%) and Candidatus Contendobacter (3.40%). As described from the denitrifying genes perspective, with the exception of nitrite reduction (performed by denitrifiers), denitrifying phosphorus-accumulating organisms (DPAOs) played a leading role in denitrification pathway, showing that poly-β-hydroxyalkanoates (PHA)-driven nutrients removal was the dominate process.