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The feasibility of a synergistic endogenous partial denitrification-phosphorus removal coupled anammox (SEPD-PR/A) system was investigated in a modified anaerobic baffled reactor (mABR) for synchronous carbon, nitrogen, and phosphorus removal. The mABR comprising four identical compartments (i.e., C1–C4) was inoculated with precultured denitrifying glycogen-accumulating organisms (DGAOs), denitrifying polyphosphate-accumulating organisms, and anammox bacteria. After 136 days of operation, the chemical oxygen demand (COD), total nitrogen, and phosphorus removal efficiencies reached 88.6 ± 1.0, 97.2 ± 1.5, and 89.1 ± 4.2%, respectively. Network-based analysis revealed that the biofilmed community demonstrated stable nutrient removal performance under oligotrophic conditions in C4. The metagenome-assembled genomes (MAGs) such as MAG106, MAG127, MAG52, and MAG37 annotated as denitrifying phosphorus-accumulating organisms (DPAOs) and MAG146 as a DGAO were dominated in C1 and C2 and contributed to 89.2% of COD consumption. MAG54 and MAG16 annotated as Candidatus_Brocadia(total relative abundance of 16.5% in C3 and 4.3% in C4) were responsible for 74.4% of the total nitrogen removal through the anammox-mediated pathway. Functional gene analysis based on metagenomic sequencing confirmed that different compartments of the mABR were capable of performing distinct functions with specific advantageous microbial groups, facilitating targeted nutrient removal. Additionally, under oligotrophic conditions, the activity of the anammox bacteria-related genes of hzswas higher compared to that of hdh. Thus, an innovative method for the treatment of low-strength municipal and nitrate-containing wastewaters without aeration was presented, mediated by an anammox process with less land area and excellent quality effluent.