As one of the most promising renewable energy, microalgal biodiesel has been widely studied worldwide. However, the low-efficiency of conventional microalgae cultivation procedures restrict the development of microalgae biodiesel production. Microalgal-bacterial symbiosis could both enhance the growth of algal-bacterial culture and promote the removal and conversion of wastewater nutrients. In this study, three strains of high-efficient heterotrophic ammonia-oxidizing bacteria JN1, FN3, and FN5 were screened from municipal wastewater treatment system with over 80% degradation rates of 50 mg/L ammonia-nitrogen (NH3–N) in 24 h. Among them, FN5, belonging to Kluyvera sp., had the optimum effect on enhancing growth of oil-rich microalga Chlorella pyrenoidosa. In stationary phase, the biomass and lipid content of Chlorella pyrenoidosa was14.8% and 13.6% higher than the blank control tests without FN5. In contrast, JN1 and FN3 failed to enhance the growth of Chlorella pyrenoidosa. After the cultivation of Chlorella pyrenoidosa-FN5 consortia in municipal wastewater, the degradation rate of NH3–N was up to 91% while the content of microalgae biomass and lipid attained 0.35 g/L and 39.0%. The Saturated fatty acids (SFAs), Monounsaturated fatty acids (MUFAs), and Polyunsaturated fatty acids (PUFAs) were 43.9, 37.1 and 19.0%, respectively, which had the potential for biodiesel production after pretreatment.