Air quality data from city clusters in the fast developing Yangtze River Delta (YRD) region of China during 1996-2003 were analyzed, with a cross-border transport study using the Regional Acid Deposition Model System (RegADMS). Investigations show that the annual average concentrations of SO2, NO2, PM10 are 12 to 64 , 13~57 , and 79~184 μg m-3, respectively. As the primary air pollutants in the target area, surface NO2 levels increased by 13% while PM10 levels decreased by 39% from 1996 to 2003. The surface SO2 concentration showed fluctuations during the study period, reaching a minimum in 1999 and rising again in 2003. Acid rain still remains an important atmospheric environmental issue. The frequency of acid rain was about 23.5~36.7%, and the pH value of precipitation ranged from 5.09 to 5.48, with little change in these years. Modeling studies indicated that sulfur deposition and nitrogen deposition were in the ranges 0.5-10 and 0.2-5 g m-2 yr-1, respectively; these levels exceed the critical load in some regions. The trans-boundary transport of sulfur deposition and nitrogen deposition due to SO2 and NOx emission among city clusters (Shanghai and the other 8 cities in Jiangsu Province, including Nanjing, Wuxi, Changzhou, Suzhou, Nantong, Yangzhou, Zhenjiang, Taizhou) in the YRD region was significant. The emission from Shanghai contributes 5%~29% of sulfur deposition and 3%~30% of nitrogen deposition in the 8 cities, while the 8 cities contribute 27.5% of sulfur deposition and 20.2% of nitrogen deposition in Shanghai.