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Transportation is a major sector of anthropogenic emissions in urban areas and deteriorates air quality. The surface and vertical observational data were combined with the model results to reveal its impact on the horizontal and vertical variations of pollutants during the COVID-19 lockdown period. The evident reductions in ambient PM2.5 (∼30%) and NO2 (∼50%) concentrations but a ∼25% increase in O3 concentration were observed at the transportation sites. On the vertical scale, a uniform decrease of ∼28% in PM2.5 concentrations was observed within 600 m. However, the vertical profiles of NO2 and O3 exhibited increasing vertical variation rates with concentrations varying significantly within 400 m. Meanwhile, Ox shared a similar pattern of vertical profile with O3, with a uniform increase (∼5%) within 600 m in the urban area. The WRF-CMAQ model reproduced the variations, and revealed that the reduction of transportation emissions was the key factor contributing to the increase of urban O3 and Ox due to the weakened NO titration effect. The simulated vertical profile of NO2 was featured by a decreasing curve, while that of O3 exhibited the opposite trend. We find that the transportation emissions impact vertical concentrations of NO2 and O3 within at most 400 m. The process analysis revealed that the vertical transport and horizontal transport from bay areas contributed to O3 in the urban area, while chemical processes mainly consumed it. The reduction in transportation emissions weakened the consumption and resulted in O3 accumulation during rush hours and at night. The variation of planetary boundary layer height also favored the rise of urban O3 by promoting vertical transport at daytime and trapping it at night. The reduction in NOx emissions from the transportation enhanced O3 pollution, suggesting that collaborative reductions in VOCs from multiple sectors should be conducted. This study also indicated that regional collaborations in emission reductions were necessary for comprehensive air pollution prevention.