There are several studies on the effects of emissions of highly reactive volatile organic compounds (HRVOC) from the industrial sources in the Houston-Galveston-Brazoria (HGB) area on the high ozone events during the Texas Air Quality Study (TexAQS) in summer of 2000. They showed that the modeled atmosphere lacked reactivity to produce the observed high ozone event and suggested "imputation" of HRVOC emissions from the base inventory. Byun et al. (2007b) showed the imputed inventory leads to too high ethylene concentrations compared to the measurements at the chemical super sites but still too little aloft compared to the NOAA aircraft. The paper suggested that the lack of reactivity in the modeled Houston atmosphere must be corrected by targeted, and sometimes of episodic, increase of HRVOC emissions from the large sources such as flares in the Houston Ship Channel (HSC) distributed into the deeper level of the boundary layer. We performed retrospective meteorological and air quality modeling to achieve better air quality prediction of ozone by comparison with various chemical and meteorological measurements during the Texas Air Quality Study periods in August-September 2006 (TexA QS-II). After identifying several shortcomings of the forecast meteorological simulations and emissions inputs, we prepared new retrospective meteorological simulations and updated emissions inputs. We utilized assimilated MM5 inputs to achieve better meteorological simulations (detailed description of MM5 assimilation can be found in F. Ngan et al., 2012) and used them in this study for air quality simulations. Using the better predicted meteorological results, we focused on the emissions uncertainty in order to capture high peak ozone which occasionally happens in the HGB area. We described how the ozone predictions are affected by emissions uncertainty in the air quality simulations utilizing different emission inventories and adjustments.