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Combination of adsorption by porous CaCO3 microparticles and encapsulation by polyelectrolyte multilayers via the layer-by-layer (LbL) self-assembly was proposed for sustained drug release. Firstly, porous calcium carbonate microparticles with an average diameter of 5 μm were prepared for loading a model drug, ibuprofen (IBU). Adsorption of IBU into the pores was characterized by ultraviolet (UV), infrared (IR), thermogravimetric analysis (TGA), Brunauer–Emmett–Teller (BET) experiment and X-ray diffraction (XRD). The adsorbed IBU amount Γ was 45.1 mg/g for one-time adsorption and increased with increasing adsorption times. Finally, multilayer films of protamine sulfate (PRO) and sodium poly(styrene sulfonate) (PSS) were formed on the IBU-loaded CaCO3 microparticles by the layer-by-layer self-assembly. Amorphous IBU loaded in the pores of the CaCO3 microparticles had a rapider release in the gastric fluid and a slower release in the intestinal fluid, compared with the bare IBU crystals. Polyelectrolyte multilayers assembled on the drug-loaded particles by the LbL reduced the release rate in both fluids. In this work, polymer/inorganic hybrid core-shell microcapsules were fabricated for controlled release of poorly water-soluble drugs. The porous inorganic particles are useful to load drugs in amorphous state and the polyelectrolyte multilayer films coated on the particle assuage the initial burst release.