Based on the reactor unstable and low nitrogen removal rate when Partial Nitritation and Anammox (PN/A) process treat municipal wastewater, a new composite bioreactor named sequencing batch-baffled-separate membrane bioreactor (SASMBR) was designed and manufactured. This reactor was applied to the treating of municipal wastewater using PN/A process to explore the performance and analyze the operating costs of the reactor. The results showed that highly efficient and stable denitrification processes had been achieved using PN/A process in this reactor, with TN removal rate up to 80%–85%, nitrogen removal rate (NRR) up to 0.20–0.22 kgN/(m3·d) and the effluent TN concentration was below 8 mg/L. 16SrRNA gene sequencing analysis found that the baffles set inside the bioreactor could enrich ammonia oxidation bacteria (AOB), which ensuring a good treating performance of the reactor. Non-woven fabrics in the SASMBR could effectively retain anaerobic ammonium oxidizing bacteria (AnAOB), and the increasing abundance of AOB in the SASMBR could provide anaerobic environment and NO₂^--N substrate for the growth of AnAOB. As such, the combination inevitably accelerated the quick startup of the reactor and maintained its highly efficient and stable running. The operating costs was 0.307 yuan/m³ which was significantly lower than the traditional municipal wastewater treatment plants.