A large calculation error of pollutant emission flux occurs due to the influence of multiple scattering when we utilize the mobile differential optical absorption spectroscopy (DOAS), which is based on the passive differential optical absorption spectroscopy, to measure the pollutant source. The concentration of NO2 that lies in the total layer increases significantly because of multi scattering in the lower atmospheric cloud. This results in large computing error of NO2 emission flux. To solve this problem, a new method is proposed. The information of O4 and SO2 vertical column density is employed during the measurement and then used to adjust the enhancement of NO2 due to multi scattering in the process of calculating flux. The experimental data from a certain Shanghai industrial district on Oct. 9th, 2010 is retrieved using this method. The flux value is 1.49 t/h and 0.5 t/h before and after correction, respectively. The results indicate that this method could effectively eliminate the influence of column density rise caused by multi scattering during the measurement. This novel method could facilitate the application of mobile DOAS on accurate measurement of emission flux from pollutant source.