Rapid urbanization has led to increased environmental pollution in Vietnam, especially air pollution issues. In this study, we used gas chromatography-mass spectrometry with an automated identification and quantification system database to detect and quantitate compounds in atmospheric fine particulate matter (PM2.5). A total of 288 compounds classified in 19 pollutant categories based on their origins were detected in PM2.5 samples collected in three areas of Hanoi during winter. The total content of substances detected ranged from 41.08 to 795.00 ng.m−3. The characteristics and concentrations of organic pollutants differed among the industrial, urban, and agricultural sampling areas, with average concentrations of 179.00, 112.10, and 529.40 ng.m−3, respectively. In this comprehensive study on trace organic compounds conducted with samples collected at three sites, we investigating the basic impact of three main factors on the environment. This study contributes to the literature by providing a data set on the content of trace organic substances in the air at the study site.