Herein, a facile and generic method is developed to prepare ultrathin, robust nanohybrid capsules by manipulating the dynamic structure of supramolecular nanocoatings on CaCO sacrificial templates by incorporating a multivalent-anion substitution process into biomineralization. Above the biomineralization level, multivalent anions, for example, phosphate, sulfate, or citrate, are used to initiate the assembly of polyamine into continuous (nonsegregated) polyamine-anion supramolecular nanocoatings on CaCO sacrificial templates. When contacting with the sodium silicate solution, the multivalent anions in the supramolecular nanocoatings are substituted by silicate because of the difference in dissociation behavior, facilitating the structure-reconstruction of supramolecular nanocoatings. At the biomineralization level, the substituted silicate can not only bind to the polyamine through electrostatic and hydrogen bonding interactions but also undergo silicification to generate an interpenetrating silica framework. After dissolution of CaCO, polyamine-silica nanohybrid capsules bearing an ultrathin wall of ∼10-17 nm in thickness are formed, which exhibit a super-high mechanical strength of ∼2337 MPa in elasticity modulus. The capsules are then utilized for bioreactor construction by encapsulating glucose oxidase. The ultrathin capsule wall facilitates the diffusion of substrates/products and elevates the conversion efficiency, whereas the high mechanical strength ensures the structural integrity of the capsules during multiple-cycle reactions. This method can also be applied for the preparation of ultrathin films on planar substrates, which would open a feasible way to prepare nanohybrid materials with different compositions and shapes.