Microalgae consortium is a promising technology for achieving low-carbon and resource utilization goals in municipal wastewater treatment. However, little is known about how the consortium affects the treatment performance in the startup stage of co-cultivation. Herein, photobioreactors were constructed with different contents of microalgae and activated sludge (AS) (wt._microalgae: wt._AS ≥ 50 %). The results showed that the concentration of microalgae increased by more than 20 % with AS, and the effluents were close or lower than Chinese discharge standards within HRT 24 h (NH₄⁺-N, TP, and COD ≤ 5.0, 0.5, and 50 mg L^-1). Furthermore, the co-occurrence pattern of microbial populations experienced inhibition-reconstruction and reconstruction-inhibition processes, respectively, and the inter-species relationship was directly related to the effluent quality. Microalgal concentration and temperature were the key factors to the microbial community profiling. The potential microorganisms in AS could promote the growth of microalgae, and the bacteria and fungi formed co-metabolism through functional complementation.