Indigenous bacteria popularly exist in real wastewater. Therefore, the potential interaction between bacteria and microalgae is inevitable in microalgae-based wastewater treatment systems. It is likely to affect the performance of systems. Accordingly, the characteristics of indigenous bacteria is worth serious concerning. Here we investigated the response of indigenous bacterial communities to variant inoculum concentrations of Chlorococcum sp. GD in municipal wastewater treatment systems. The removal efficiency of COD, ammonium and total phosphorus were 92.50%–95.55%, 98.00%–98.69%, and 67.80%–84.72%, respectively. The bacterial community responded differently to different microalgal inoculum concentrations, which was mainly affected by microalgal number, ammonium and nitrate. Besides, there were differential co-occurrence patterns and carbon and nitrogen metabolic function of indigenous bacterial communities. All these results indicated that bacterial communities responded significantly to environmental changes caused by the change of microalgal inoculum concentrations. The response of bacterial communities to different microalgal inoculum concentrations was beneficial for forming a stable symbiotic community of both microalgae and bacteria to remove pollutants in wastewater.