The rapid start-up and operating characteristics of simultaneous partial nitrification, anammox, and denitrification (SNAD) process was investigated using synthetic wastewater with a low C/N ratio (COD: NH4+-N = 200 mg/L: 200 mg/L) in a novel upflow microaerobic membrane bioreactor (UMMBR). The average removal efficiencies of COD, NH4+-N, and TN in the stable phase were 89%, 96%, and 86%, respectively. Carmine granule, which coexisted with sludge floc, appeared on day 83. The high sludge concentration (12.9–17.2 g/L) and the upflow mode of the UMMBR could establish some anaerobicregions for anammox process. The anammox bacteria and short-cut denitrification (NO2−→N2) bacteria with activities of 4.46 mg NH4+-N/gVSS·h and 2.57 mg NO2−-N/gVSS·h contributed TN removal of 39% and 61% on day 129, respectively. High-throughput sequencing analysis revealed that the ammonia-oxidizing archaea (AOA, 49.45% in granule and 17.05% in sludge floc) and ammonia-oxidizing bacterial (AOB, 1.30% in sludge floc) dominated the nitrifying microbial community. Candidatus Jettenia (47.14%) and Denitratisoma (10.92%) mainly existed in granule with positive correlations. Some heterotrophic bacteria (OLB13, SJA-15, 1–20, SBR1031, and SJA-28) in sludge floc benefited system stability and sludge activity and protected Candidatus Jettenia from adverse environments. Display omitted •Rapid start-up of SNAD was obtained with high removal of TN(86%) and COD(89%).•Sludge floc and anammox granule coexisted in this novel UMMBR.•High sludge concentration and upflow mode were important in rapidly attaining SNAD.•AOA(49.45% in granule, 17.05% in floc) dominated nitrifying microbial community.•Candidatus Jettenia (47.14%) and Denitratisoma (10.92%) mainly existed in granule.