In this paper, a four nested Weather Research and Forecasting-Community Multiscale Air Quality (WRF-CMAQ) model was applied to analyze ozone (O3) concentration reductions under the influence of extremely high NOx concentrations emitted from ships at the Hankou Jiangtan (HJ) station adjacent to the Yangtze River in Wuhan, China. By adding NO emissions along the waterway for the sensitivity experiments, the model successfully reproduced two cases of high NOx concentrations on April 9 and April 28, 2020, and one case of persistent and extremely high NOx concentrations on the night of May 3, 2020. During daytime, strong photochemical reactions generated new O3, while the high concentration NOx from ship emissions continuously reduced O3 through catalytic cycling. This led to the O3 concentrations at the HJ station being consistently lower than the surrounding stations in the afternoon, with the high NOx plume dropping O3 concentrations by 51 ppb in 1 h, and NO2 concentrations up to 110 ppb. The presence of large amounts of fresh NO (up to 265 ppb) in the ship emission plumes rapidly reduces O3 concentrations through titration reactions during night, resulting in a wide area of low O3 concentrations (2–4 ppb) over a long period of time. This study demonstrates that the pollution and impact of emissions from ships traveling in waterways on the atmosphere of the surrounding area cannot be ignored.