By AFM we report the successful modulation of shell structure (morphology and shell thickness) of microcapsules through tailoring molecular substituents of chitosan. The shell thickness of hollow (HPCS/SA)(n) (n = 5, 7, 9) capsules is more than 3 times that of the (QACS/SA)(n) (n = 5, 7, 9) capsules, due to less charges carried by the neutral -NH2 substituent group and the induced coily conformation in HPCS, while more charges carried by the positively charged -N(CH3)(3)(+) substituent and the induced extended conformation in QACS (HPCS: hydroxyl propyl chitosan; QACS: quaternary ammonium chitosan; SA: sodium alginate). The ultrathin shells of microcapsules assembled in this work by the layer-by-layer (LbL) self-assembly technique rather than the traditional method of mixing CS, SA and CaCl2 enable the thickness modulation characterization by AFM on the atomic scale. These microcapsules with tunable shell thickness provide important guidance for potential drug delivery and sustained release. (C) 2012 Elsevier Inc. All rights reserved.