The Houston air quality has been improving due to various pollution control measures implemented since the TexAQS 2000, but the area still suffers significant ozone nonattainment problems. There are serious uncertainties in the anthropogenic hydrocarbon emissions and other sources of atmospheric radicals. Complex coastal meteorology and its interaction with chemistry pose significant scientific challenges to understand the atmospheric processes and to help improve air quality modeling and forecasting skills and pollution control measures. The Texas Air Quality Field Study II (TexAQS II) in August - October 2006 was a comprehensive research initiative to better understand the causes of air pollution. The main objective of the project was to understand emissions and processes associated with the formation and transport of ozone and regional haze in Texas. We performed retrospective MM5 meteorological modeling with muti-nesting data assimilation method and evaluated CMAQ air quality simulations with in-situ atmospheric chemical measurements. The muti-species photochemical relations observed were replicated with successful retrospective meteorological simulations.