It has been reported that ambient ozone concentrations in Japan have not been effectively suppressed by precursor emission controls. In this study, we developed an unprecedented long-term emission inventory of ozone precursors, including nitrogen oxide (NOX) and volatile organic compounds (VOCs), in Japan. The developed emission inventory, which explicitly represents changes in emissions caused by emission controls and variation in activities from 2000 to 2019, revealed that emission controls implemented for vehicles, large point sources, and fugitive VOC sources effectively reduced precursor emissions. The impact of emission changes on ozone concentrations at six different timescales was evaluated using air quality simulations. Three of them corresponded to annual mean values of daily ozone concentrations, and the others corresponded to annual high ozone concentrations. The simulations performed better at higher ozone concentrations. The simulation results suggested that emission controls have helped suppress annual high ozone concentrations, whereas the annual mean values of daily ozone concentrations may have increased in populated urban areas because reduced NOX emissions weakened the titration of ozone. Overall changes in the simulated ozone concentrations over different timescales were generally consistent with those in the observed ozone concentrations. These findings highlight the importance of evaluating the impact of emission controls on ozone concentrations over multiple timescales. The differences in the sensitivities of ozone concentrations to emission controls were clearly explained by the ozone sensitivity regimes implied by the ratios of formaldehyde to nitrogen dioxide. The outcomes of this study could assist countries beyond Japan in developing effective strategies to manage ozone pollution.