Nitrated aromatic compounds (NACs) are toxic and allergenic airborne pollutants from both primary emissions and atmospheric reactions of aromatics with NO2. A comprehensive investigation of NACs is challenging given their low ambient levels. By applying gas chromatography and tandem mass spectrometry coupled with an electron capture negative ionization source, this study achieved a comprehensive high-throughput and standard-independent detection of nonpolar NACs in fine particulate matter (PM2.5) sampled over 2 years in Beijing, China. Overall, 1047 NACs were detected, among which, the elemental composition of 128 species were derived using time-of-flight mass spectrometry, and 25 species were confirmed using reference standards. In addition to mono-nitrated polycyclic aromatic hydrocarbons (NPAHs), di-nitrated PAHs and alkylated and oxygenated NPAHs were found. Cluster analysis suggested these compounds were derived from various sources particularly atmospheric reactions. We found that the annual levels of primary NPAHs decreased by 46.3–54.8% from 2012–2013 to 2016–2018, though the secondary species did not change significantly after normalization by PM2.5. These results were validated by diagnostic ratios, which indicated an increasing contribution from the secondary formation including nighttime reactions. This novel method for NACs detection may provide valuable insights into the formation mechanisms of NACs in the atmosphere.