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Indoor air quality (IAQ) of urban public transportation stations (UPTS) has adverse health impacts on the station employees and commuters. However, there is a lack of comprehensively evaluations of IAQ in waiting rooms of UPTS. Therefore, it is crucial to select appropriate air quality indexes (including fuzzy synthetic index (B), comprehensive index (P), I 1 index, and indoor air quality index (IAQI)) to assess air quality and potential health risks. Our study is a subsample of the CPPEHS 2019 study, which included 224 UPTS in 126 cities of China. We found that P index showed an excellent air quality rate of 95.96% in the railway stations and 83.19% in the inter-city bus stations. The P index was correlated with UPTS usage years, useable area, and per passenger useable area. Furthermore, waiting rooms in UPTS with good (OR = 1.9187, 95% CI: 1.1204, 3.2859) and bad (OR = 2.0854, 95% CI: 1.2182, 3.5698) air quality evaluated by P index had a higher risk of rhinitis compared to those with excellent air quality. Similarly, UPTS with good (OR = 2.2202, 95% CI: 1.3427, 3.6711), bad (OR = 1.7897, 95% CI: 1.0807, 2.9637), and serious (OR = 1.7478, 95% CI: 1.0098, 3.0250) air quality evaluated by P index were associated with a higher risk of pharyngitis. These findings suggested that P index is the optimal index for assessing air quality in UPTS, while IAQI may exaggerate indoor air pollution and the B index may underestimate it. Overall, this study aims to identify and evaluate the more suitable air quality index (P) in nationwide UPTS, providing valuable insights for control of IAQ and guiding the air quality management and standards. • The evaluation of indoor air quality in urban public transportation stations (UPTS) currently lacks a reliable index. • Four indoor air indexes were calculated to evaluate the air quality of UPTS. • Comprehensive index (P) is the optimal index to evaluate the air quality and health risks in UPTS. [ABSTRACT FROM AUTHOR]