Atmospheric pollution has become a global environmental issue, which caused a number of human health threats. It is therefore vital to understand the source-sink processes of air pollutants and their mechanisms. Rainwater is not only the major sink (removal process) of air pollutants, but also the good source tracer of atmospheric components. On the background of global climate changes, the extreme rainfall exerts a serious influence in megacity. However, the extreme rainfall driven chemical evolution of rainwater and its reflection on air pollution are rarely focused, even though it plays a significant role in urban-surficial ecosystem. To better understand the chemical evolution of urban extreme rainfall and their potential environmental effects, rainwater samples were collected in Beijing, a typical megacity, during the extreme rainfall period in 2021. Based on rainwater stoichiometry and historical comparison, the scouring process of air substance, the neutralizing process of rainwater and the ion sources were revealed. The findings showed that NH4+, NO3−, SO42−, and Ca2+ were four primary rainwater ions with distinct daily variations which were well removed by rainwater scouring process. The high values of NF (neutralization factor, ∼2.2) and NP/AP (ratio of neutralizing to acidifying potential, ∼1.8) suggested a relatively high level of rainwater neutralization. Source identification revealed that rainwater SO42− (94.9%) and NO3− (99.9%) were primarily originated from anthropogenic input, particularly the mobile emission sources (transportation), while sea salt input represented the major Cl− source (86.9%) and all Na+ source. By contrast, crust dust input was the main contributor of rainwater K+ (94.0%), Mg2+ (92.3%) and Ca2+ (98.2%), whereas NH4+ was considered only the contribution of human input (e.g., municipal feces and fossil fuel burning). This study clarified the chemical characteristics of extreme rainfall in megacity and highlighted the significant impact on urban environment, which will benefit the urban environmental management in the context of global climate change.