We report the exfoliation of two‐dimensional polyoxometalate‐encapsulating MOF (POM−Co‐MOF) into atomically thick nanosheets for highly efficient desulfurization application. Two‐dimensional layer‐structured MOF [Co2(H2O)4(BTX)3][PMo12O40] (BTX=1,4‐Bis(1,2,4‐triazol‐1‐ylmethyl)benzene) is featured with Keggin‐type POM wrapped in MOF skeleton via coordinating to cobalt with terminal oxygen. Wet ball‐milling and sonication assisted top‐down exfoliation in acetonitrile successfully delaminates POM‐MOF into nanosheets, which creates more accessible active sites and efficiently decreases the restriction of mass transfer during the reaction, and thus enhances the desulfurization efficiency. In comparison with bulk POM‐MOF, delaminated nanosheets exhibit a 14‐fold higher desulfurization efficiency via monitoring dibenzothiophene oxidation process (TON value of ca. 400) using H2O2 as oxidant. Meanwhile, POM−Co‐MOF nanosheets also show superior desulfurization performance in model oil system.