In this study, the CALPUFF/MM5 modeling system was applied to estimate the air quality impacts of elevated point sources in 2004 in Chongqing. An intercomparison of the performance of CALPUFF against the observed data is discussed and an examination of scatter plots and QQ plots is provided. Results show that in 2004 the high emission contribution induced a relatively high contribution to average ambient concentration and significant impact on the urban area (higher than 10 μg/m3 of 24-hour averaged SO2 concentration, maximum of 650 μg/m3). The highest 24-hour averaged SO2 concentration exceeds the Grade NAAQS by 10.6%, 153.3%, 60% and 333.0% for January, April, July and October, respectively. The concentration distributions demonstrate the heterogeneity patterns in spatial and temporal scales due to significant topographic diversity and weather variations over short distances. The source of the SO2 in the Chongqing area is local air pollution, which results from the lower effective stack height, low wind velocity in the area, basin topography, and the use of coal with high sulfur content. Parametric sensitivity analyses are still needed to determine the magnitude of uncertainty associated with CALPUFF.