It is desirable to develop new materials that can efficiently lower sulfur content in fossil fuels, such as gasoline and diesel oil. Polyoxometallic acids supported on metal–organic frameworks (MOFs) are an important class of heterogeneous catalysts for oxidative desulfurization. However, there has been no comprehensive study on the correlation between desulfurization activity and the window size of MOFs. A series of robust MOFs, which include MIL‐100(Fe), UiO‐66, and ZIF‐8, with different window sizes were exploited as hosts to encapsulate phosphotungstic acid by the “bottle around the ship” method and utilized for the ultra‐deep oxidative desulfurization (ODS) of model and real gasoline. Compared with UiO‐66 and ZIF‐8, which have very small window sizes, mesoporous MIL‐100(Fe), which has a large window size, exhibited the best catalytic performance in the ODS of refractory sulfur compounds (benzothiophene, dibenzothiophene, and 4,6‐dimethyl‐dibenzothiophene) and in recycling experiments. The correlations between the desulfurization activity and the window size of the corresponding MOFs could provide insights for the design of new porous catalysts for ODS and other size‐selective catalysis reactions in the future.