The Keggin‐type polyoxometalates (POMs) are effective catalysts for oxidative desulfurization (ODS) and confining these POMs in metal–organic frameworks (MOFs) is a promising strategy to improve their performances. Herein, postsynthetic modification of POMs confined in MOFs by adding thiourea creates more unsaturated metal sites as defects, promoting ODS catalytic activity. Additional modification by confining 1‐butyl‐3‐methyl imidazolium POMs in MOFs is performed to obtain higher ODS activity, owing to the affinity between electron‐rich thiophene‐based compounds and electrophilic imidazolium compounds. The ODS catalytic activities of four Zr‐MOF‐based composites (bottle around ship) including phosphomolybdate acid (PMA)/UiO‐66, Bmim3PMo12O40/UiO‐66, PMA/Thiourea/UiO‐66, and Bmim3PMo12O40/Thiourea/UiO‐66 are therefore investigated in detail. In order to explore the catalytic mechanism of these MOF composites, their microstructures and electronic structures are probed by various techniques such as X‐ray diffraction, thermogravimetric analysis, Fourier transform infrared, Raman, scanning electron microscope, transmission electron microscope, BET, X‐ray photoelectron spectroscopy, EPR, UV–vis, NMR spectra, and H2‐temperature‐programmed reduction. The results reveal that phosphomolybdate blues and imidazolium phosphomolybdate blues with different Mo5+/Mo6+ ratios with the Keggin structure are confined in defected UiO‐66 for all four composites. This approach can be applied to design and synthesize other POMs/MOFs composites as efficient catalysts. A design strategy aims to form phosphomolybdate blues confined in defected Zr‐metal–organic framework (MOF) by adding thiourea, which can produce oxygen vacancies with electrons trapped in and Mo5+ to promote the catalytic activity. Moreover, 1‐butyl 3‐methyl imidazolium phosphomolybdate blues are confined in Zr‐MOF to obtain higher oxidative desulfurization activity owing to the affinity between electron‐rich thiophene‐based compounds and electrophilic imidazolium compounds.