To optimize the highly stacked, lamellar covalent organic frameworks (COF) with more easily accessible micropores for molecular separations, a facile and economical strategy, using the naturally available diatomite (Dt) as a substrate, is proposed to fabricate hierarchical Dt@COF hybrids through an in-situ solvothermal method to grow a uniform COF shell on Dt. This strategy not only enormously enhances the adsorption capacity of diatomite through introducing abundant micropores, but also endows the grown COFs with highly accessible adsorption sites for molecular adsorption owing to the ultrathin COFs shell and the intrinsic porosity of the diatomite matrix. The maximum adsorption capacity of COFs from Dt@COF-0.04 is 686 mg g−1 toward bisphenol A (BPA), outperforming the bulk COFs adsorbent (∼381 mg g−1). Significantly, in a more convenient column separation mode, the equilibrium adsorption amount of Dt@COF-0.04 is ∼3 times greater than that of the COF/Dt mixture. It is found that the thin COFs shell and the intrinsic microchannels of diatomite nanoplates synergistically facilitate the diffusion of water molecules and pollutants, leading to the outstanding performance of Dt@COF adsorbents. The results indicate that the hierarchical Dt@COF hybrids have great application potential in the separation of organic pollutants from water for environmental remediation.