In recent years, China has adopted numerous policies and regulations to control NOx emissions to further alleviate the adverse impacts of NO3−-N deposition. However, the variation in wet NO3−-N deposition under such policies is not clear. In this study, the southeastern area, with highly developed industries and traditional agriculture, was selected to explore the variation in NO3−-N deposition and its sources changes after such air pollution control through field observation and isotope tracing. Results showed that the annual mean concentrations of NO3−-N in precipitation were 0.67 mg L−1 and 0.54 mg L−1 in 2014–2015 and 2021–2022, respectively. The average wet NO3−-N depositions in 2014–2015 and 2021–2022 was 7.76 kg N ha−1 yr−1 and 5.03 kg N ha−1 yr−1, respectively, indicating a 35% decrease. The δ15N–NO3− and δ18O–NO3− values were lower in warm seasons and higher in cold seasons, and both showed a lower trend in 2021–2022 compared with 2014–2015. The Bayesian model results showed that the NOx emitted from coal-powered plants contributed 53.6% to wet NO3−-N deposition, followed by vehicle exhaust (22.9%), other sources (17.1%), and soil emissions (6.4%) during 2014–2015. However, the contribution of vehicle exhaust (33.3%) overpassed the coal combustion (32.3%) and followed by other sources (25.4%) and soil emissions (9.0%) in 2021–2022. Apart from the control of air pollution, meteorological factors such as temperature, precipitation, and solar radiation are closely related to the changes in atmospheric N transformation and deposition. The results suggest phased achievements in air pollution control and that more attention should be paid to the control of motor vehicle exhaust pollution in the future, at the same time maintaining current actions and supervision of coal-powered plants.