For fabricating a hydrogen-bonded framework with a stabilized hybrid structure for versatile functional properties, an inorganic polyanionic cluster that bears covalently grafted organic groups for hydrogen bond connection is synthesized. By modifying two guanine groups into a disklike polyoxometalate [Mn(OH)6Mo6O18]3- on both sides symmetrically, a polyanionic hybrid building block is obtained. With the cluster serving as a bridge and the grafted guanine unit serving as the binding sites, a polyoxometalate built-in hydrogen-bonded framework in the form of a square lattice shape within a two-dimensional plane has been fabricated as a single-layer assembly. In a further step, the counterion connection and hydrophilic/hydrophobic effect are used to drive the growth of layered framework assembly along the perpendicular direction. The resulting cluster-embedded framework possesses permanent porosity and inner-layer ionic characteristics after activation, which allows the framework to exhibit both high charge-/size-selective adsorption of organic cations and pH-controlled catalytic oxidation of methionine via the charged property.