Multilayer microcapsules showing unique charge-controlled permeability have been successfully fabricated by employing poly(styrene sulfonate) (PSS)-doped CaCO3 particles as templates. Encapsulation of the PSS molecules is thus achieved after core removal. Scanning force microscopy (SFM), UV-vis, Raman spectroscopy, and zeta-potential confirm the existence of the PSS molecules in the CaCO3 particles and the resultant microcapsules, which are initially incorporated during the core fabrication process. A part of these additionally introduced PSS molecules interacts with PAH molecules residing on the inner surface of the multilayer wall to form a stable complex, while the other part is intertwined in the capsule wall or in a free state. Capsules with this structure possess many special features, such as highly sensitive permeability tuned by probe charge and environmentally controlled gating. They can completely reject negatively charged probes, but attract positively charged species to form a higher concentration in the capsule interior, as evidenced by confocal microscopy. For example, the capsules completely exclude dextran labeled with fluorescein isothiocyanate (FITC-dextran), but are permeable for dextran labeled with tetramethylrhodamine isothiocyanate (TRITC-dextran) having similar molecular mass (from 4 to 70 kDa), although there are only few charged dyes in a dextran chain. By reversing the charge of the probes through pH change, or by suppressing charge repulsion through salt addition, the permeation can be readily switched for proteins such as albumin or small dyes such as fluorescein sodium salt.