The migration of enhancements in NO2 and O3 concentration and radiative effects associated with the onset of the North American Monsoon in summer has been investigated using satellite data and the regional chemical transport model (CTM). Also, simulations results from CTM and satellite data in summer are analyzed to estimate the uncertainty of the EPA National Emissions Inventory over six geological regions (e.g., Pacific Coast, Rocky Mountain, Low Middle, Upper Middle, Southeast, and Northeast). The satellite data include the tropospheric NO2 columns, tropospheric O3 profiles, and OLR from OMI, TES and NOAA-16 satellite, respectively, for June and July 2005 and GOME-2 NO2 columns for August 2009. The first study reveals that lightning-generated NOx exerts a smaller impact on tropospheric NOx and O3, but a larger, by up to a factor of three, impact on radiative impact by enhancing O3 in the upper troposphere than anthropogenic NOx that increase O3 in the lower troposphere. By comparing GOME-2 NO2 columns to CTM columns, we found from the second study that satellite-adjusted NOx emissions significantly decreased over Low Middle of US, which resulted in large reduction in surface NOx. The large reductions in NOx emissions mitigate the discrepancies of surface NOx concentrations at EPA measurement stations between CMAQ and AQS. This study indicates high NOx biases of the EPA National Emission Inventory over Low Middle, which could shed light on this bias issue from various global/regional CTMs.