<p>Activity, abundance, and synergy of functional microorganisms are pivotal for wastewater treatment. Here, we developed a micron-medium biofilm composite sludge system, integrating powder carriers and a hydrocyclone separator to enhance functional bacterial enrichment and micro-granule formation. Powder carriers acted as bridges between zoogloea, facilitating coexistence of micro-granules (~115.8 μm) and suspended flocs, thereby improving microbial synergy. The pilot-scale system doubled treatment capacity without expansion or downtime, achieving effluent total nitrogen &lt;5 mg L⁻¹ and total phosphorus &lt;0.3 mg L⁻¹ at a hydraulic retention time of 4.85 h. Micro-granules enhanced sludge settleability, mass transfer, and endogenous carbon metabolism, including polyhydroxyalkanoate and glycogen synthesis, which provided essential electron donors for nutrient removal. Denitrifying and phosphorus-accumulating bacteria were enriched in micro-granules (4.46%), whereas nitrifying bacteria (1.25%) were concentrated in flocs. Differentiated spatial distribution balanced the sludge age conflict among functional bacteria. This work provided an efficient and low-carbon strategy for municipal wastewater treatment.</p><p></p>