Accurate estimates of NOx and SO2 emissions are important for air quality modeling and management. To incorporate chemical interactions of the two species in emission estimates, we develop a joint hybrid inversion framework to estimate their emissions in China and India (2005–2012). Pseudo observation tests and posterior evaluation with surface measurements demonstrate that joint assimilation of SO2 and NO2 can provide more accurate constraints on emissions than single‐species inversions. This occurs through synergistic change of O3 and OH concentrations, particularly in conditions where satellite retrievals of the species being optimized have large uncertainties. The percentage changes of joint posterior emissions from the single‐species posterior emissions go up to 242% at grid scales, although the national average of monthly emissions, seasonality, and interannual variations are similar. In China and India, the annual budget of joint posterior SO2 emissions is lower, but joint NOx posterior emissions are higher, because NOx emissions increase to increase SO2 concentration and better match Ozone Monitoring Instrument SO2 observations in high‐NOx regions. Joint SO2 posterior emissions decrease by 16.5% from 2008 to 2012, while NOx posterior emissions increase by 24.9% from 2005 to 2011 in China—trends which are consistent with the MEIC inventory. Joint NOx and SO2 posterior emissions in India increase by 15.9% and 19.2% from 2005 to 2012, smaller than the 59.9% and 76.2% growth rate using anthropogenic emissions from EDGARv4.3.2. This work shows the benefit and limitation of joint assimilation in emission estimates and provides an efficient framework to perform the inversion.