Novel molecular-recognizable smart microcapsules for controlled release are successfully fabricated in two steps. Firstly, monodispersed poly(N-isopropylacrylamide-co-acrylic acid) microcapsules are prepared via microfluidic emulsion template synthesis; and then, beta-cyclodextrin groups are introduced onto the microcapsules by a condensation reaction. The results of Fourier transform infrared spectrometry confirm that beta-cyclodextrin moieties are successfully immobilized onto microcapsules by the condensation reaction between carboxylic groups of acrylic acid components on the microcapsules and amino groups of modified beta-cyclodextrin monomers. The resultant poly(N-isopropylacrylamide-co-acrylic acid/aminated beta-cyclodextrin) (PNA-ECD) microcapsules show a narrow size distribution. The volume phase transition temperature of prepared PNA-ECD microcapsules exhibits a positive shift in the solution containing model guest molecules 2-naphthalenesulfonic acid (NS). Upon recognizing the guest molecules NS, the PNA-ECD microcapsules show an isothermal and reversible molecular-recognizable swelling behavior. Moreover, the release rate of model drug molecules Fluorescein isothiocyanate-labeled dextran loaded in the microcapsules dramatically increases upon recognizing NS molecules. The results provide valuable guidance for the design and fabrication of monodispersed molecular-recognizable microcapsules for controlled release.