Carbon dioxide reduction technologies using photosynthetic microorganism were suggested to overcome environmental destruction caused by $CO_2$ in flue gases from power plant and other industries. However, there are many toxic constituents in flue gas including CO, NOx, SOx. Continuous and Excessive supply of these noxious gases to cells will leads to inhibition of microalgal growth along with partial cell death. In this study, we tested the noxious effect of SOx and NOx on the pH and microalgal growth under photoautotrophic culture in three microalgae of Neochloris oleoabundans, Chlorella vulgaris and Haematococcus pluvialis. As a result, SOx concentration more than 50 ppm led to the rapid reduction of pH, thereby inhibiting of the growth in Neochloris oleoabundans and Chlorella vulgaris. NOx concentration more the 100 ppm reduced the exponential growth of N. oleoabundans and C. vulgaris. And H. pluvialis exhibited low sensitivity to SOx and NOx. Consequently, the three microalgae of N. oleabundas, C. vulagaris and H. pluvialis showed the normal vegetative growth in 25 ppm of NOx and SOx. Above all, H. pluvialis was useful for the $CO_2$ sequestration of the flue gas including high concentrations of NOx and SOx.