Volatile organic compounds (VOCs) are major air pollutants often designated as specific hazardous or toxic. This study analyzed the trends in concentration changes and influencing factors of VOCs in underground subway stations in the Seoul Metro before (2019) and after (2021) the COVID-19 pandemic. A total of 506 samples were collected from 253 stations on lines 1–8 between May 2019 and September 2021. Total VOC concentrations in Seoul Metro increased after the COVID-19 pandemic 3.8 times over. The deeper the underground station platform, the greater the difference in the VOC concentrations between 2019 and 2021, which was positively related. Average VOC concentration was the highest (52.8 µg/m3) at a depth of 25–30 m and the lowest (23.9 µg/m3) at a depth of < 10 m in 2019. In conclusion, excessive disinfection during the COVID-19 pandemic resulted in increased VOC concentrations in the Seoul Metro, especially in the deeper underground stations. Less frequent quarantine disinfection is recommended to improve air quality.