Not only carbon dioxide (CO2) but also air pollutants, such as sulfur oxides (SOx) and nitrogen oxides (NOx), are present in flue gas, and their reasonable and effective utilization is conducive to reducing the cost of microalgal biomass production. By utilizing simulated flue gas, the absorption characteristics of different components in transfer units were explored. The results showed that the presence of SO2 decreased the absorptivity of CO2, which reduced the concentration of the available carbon source for microalgal cells in the culture medium at the same pH value. Moreover, the presence of high-concentration oxygen (O2) in flue gas could improve the absorptivity of nitric oxide (NO). Scenedesmus dimorphus was cultured by using sulfur- or nitrogen-deficient culture media. The results showed that SOx and NOx in flue gas did not significantly influence the growth and biochemical compositions of microalgal cells when these gases were dissolved in water. Based on the above results and the metabolic kinetics of microalgal cells for nutrient elements, an adjustment strategy for the initial gas source when culturing microalgae with flue gas is proposed: (1) flue gas should be partially desulfurized so that the SOx and CO2 concentrations after desulfurization satisfy a certain relationship with the components; and (2) denitrification should not be performed because flue gas can be oxidized before utilization to increase the rate of utilization of NO.