Oxidative desulfurization is considered to be one of the most promising methods for producing ultra-low-sulfur fuels because it can effectively remove refractory sulfur-containing aromatic compounds under mild conditions. In this work, the oxidative desulfurization performance over UiO-66(Zr) is greatly enhanced by Ti ion exchange. This strategy is not only efficient for UiO-66(Zr) with crystal defects but also for UiO-66(Zr) with high crystallinity. In particular, the performance of UiO-66(Zr) with high crystallinity in the oxidative desulfurization of dibenzothiophene can be improved more than 11-fold, which can be mainly attributed to the introduction of active Ti sites.