Background CO2 emission, water pollution and petroleum shortage are the issues coming with the development of industry. A cost effective system was constructed to fix the CO2 in flue gas (15% CO2), remove nitrogen and phosphorus from manure wastewater and produce biofuels at the same time. The significant cultivation conditions were selected by Plackett-Burman design, and then optimized with central composite design. Results Optimum culture condition was predicted at light intensity of 238 µmol·m- 2·s- 1, TN of 152 mg·L- 1, inoculum density of 0.3 g·L- 1, under which the measured CO2 fixation rate, total nitrogen and phosphorus removing rate, and lipid content were 638.13 mg·L- 1·d- 1, 88.16%, 73.98% and 11.9%, respectively. The lipid content was then enhanced to 24.2% by a nitrogen starvation strategy. Conclusion A cultivation strategy was suggested to achieve effective C/N/P removal from flue gas and manure wastewater, and meanwhile obtained high lipid content from microalgal biomass.