Acid rain has already been the environment issue for the past century and is still concerned in Southern and Eastern China. However, Northeastern China, considered in the past as non-acid rain area, is reported high frequency of acid rain occurred recently. Through a measurement and model simulation analysis with linear regression technique, factor speciation, backward trajectory, source-tracing and fraction sampling methods, this study aims to investigate the causes of the acid rain frequently occurred in the two Northeastern cities (i.e., Dandong and Dalian) and to identify the contributing sources of the chemical ions in precipitation. The annual averaged pHvwa of 2007 ranged within 4.15–4.27 and 4.5–5.15 over Dandong and Dalian, which suggested the similar acidity with Southern China. The precipitation acidity in Dandong was found to be sulfur dominant in winter-spring (nssSO42–/NO3– = 13.1) than summer-autumn (nssSO42–/NO3– = 1.05), whereas in Dalian, estimated ratio nssSO42–/NO3– was about 2.35 all over the year, reflecting the strong impact of local NOx emissions from a much more intense mobile traffic in comparison with Dandong. The findings also revealed a typical physico-chemical condition with constant strong influence of regional transport over Dandong and Dalian particularly in summer. Besides, analysis of washout and rainout mechanisms showed that the long range transport in-cloud (rainout) was more pronounced in Dandong (with minor local emissions) than Dalian (with more significant local emissions). This study indicates that acid rain pollution in Northeastern China requires much effort, not only in local emission abatement, but also in regional trans-boundary pollution control.