Comparison between the CMAQ (Community Multi-scale Air Quality Model)-calculated and OMI (Ozone Monitoring Instrument)-retrieved tropospheric NO<sub>2</sub> columns was carried out for 2006 over East Asia (100–150° E; 20–50° N) to evaluate the bottom-up NO<sub>x</sub> emission fluxes of INTEX-B, CAPSS, and REAS v1.11 inventories. The three emission inventories were applied to the CMAQ model simulations for the countries of China, South Korea, and Japan, respectively. For the direct comparison between the two NO<sub>2</sub> columns, the averaging kernels (AKs) obtained from the Royal Netherlands Meteorological Institute (KNMI)/DOMINO v2.0 daily product were applied to the CMAQ-simulated data. The analysis showed that the two tropospheric NO<sub>2</sub> columns from the CMAQ model simulations and OMI observations (Ω<sub>CMAQ,AK</sub> and Ω<sub>OMI</sub>) had good spatial and seasonal correlation, with correlation coefficients ranging from 0.71 to 0.96. In addition, the normalized mean errors (NMEs) between the Ω<sub>CMAQ,AK</sub> and Ω<sub>OMI</sub> were found to range from ~ 40 to ~ 63%. The Ω<sub>CMAQ,AK</sub> were, on annual average, ~ 28% smaller (in terms of the NMEs) than the Ω<sub>OMI</sub>, indicating that the NO<sub>x</sub> emissions used were possibly underestimated in East Asia. Large absolute differences between the Ω<sub>CMAQ,AK</sub> and Ω<sub>OMI</sub> were found, particularly over central eastern China (CEC) during winter (annual averaged mean error of ~ 4.51 × 10<sup>15</sup> molecules cm<sup>−2</sup>). Although such differences between the Ω<sub>CMAQ,AK</sub> and Ω<sub>OMI</sub> are likely caused by the errors and biases in the NO<sub>x</sub> emissions used in the CMAQ model simulations, it can be rather difficult to quantitatively relate the differences to the accuracy of the NO<sub>x</sub> emissions, because there are also several uncertain factors in the CMAQ model, satellite-retrieved NO<sub>2</sub> columns and AK products, and NO<sub>x</sub> and other trace gas emissions. In this context, three uncertain factors were selected and analyzed with sensitivity runs (monthly variations in NO<sub>x</sub> emissions; influences of different NO<sub>x</sub> emission fluxes; and reaction probability of N<sub>2</sub>O<sub>5</sub> radicals). Other uncertain or possible influential factors were also discussed to suggest future direction of the study.