In order to lower the cost of lipid production of microalgae and reduce greenhouse gas emissions, microalgae Chlorococcum alkaliphilus MC-1 with the characteristics of rapid pH drift and high pH adaptability, was cultivated with bubbling of flue gas. The experiment was first performed in the photobioreactor (15 L) in three groups (control group, CO2 group and flue gas group), then, in the open raceway pond (24 m2). The adaptability of microalgae MC-1 to the cultivation with flue gas was studied. The results showed that the maximum biomass concentration, growth rate, total lipid content and CO2 fixation rate were (1.02+/-0.07) g/L, (0.12+/-0.02) g/(L.d), (37.84+/-0.58)% and (0.20+/-0.02) g/(L.d) in the photobioreactor treated with flue gas, 36%, 33.33%, 15.34% and 33.33% higher than those of the CO2 group, respectively. In the open raceway pond with aeration of flue gas, the maximum biomass concentration, growth rate, total lipid content and CO2 fixation rate were 147.40 g/m2, 14.73 g/(m2.d), 35.72% and 24.01 g/(m2.d), respectively, which were similar to the cultivation with pure CO2. The toxic heavy metal contents (Pb, As, Cd and Cr) in the biomass of MC-1 treated with flue gas were all below the legal limits. Additionally, the absorptive effect of CO2, NO and SO2 were determined. In the photobioreactor and open raceway pond, the average absorption ratios of these gases were all higher than previous studies. Therefore, our study showed that MC-1 can adapt to the cultivation with flue gas, and it is feasible to enlarge the outdoor cultivation of MC-1 for lipid production coupling with emissions reduction of flue gas.