Hybrid microspheres from palygorskite (PAL) nanoclay and crosslinked chitosan (QS) were prepared with the emulsion method to trap and control the release of thymol (TIM). The morphology of the microspheres was characterized by scanning electron microscopy and x-ray diffraction. The size of the microspheres, the swelling rate, the encapsulation efficiency and thymol release rate were characterized. Compared to pristine chitosan microspheres, hybrid microspheres showed the highest encapsulation efficiency. The average particle sizes of the QS and QS-PAL microspheres are in a range of 20 to 50 μm, with a size distribution of the hybrid microspheres showing less size polydispersity. The QS-PAL microspheres have a higher swelling rate than the QS microspheres. The lowest swelling degree, 88%, was from the microspheres without PAL cross-linked with 950 μl of glutaraldehyde (GL), and the highest swelling degree, 146%, was from the microspheres with 10% PAL crosslinked with 630 μl of GL. The thymol release kinetics was modified by the palygorskite content of the chitosan hybrid microspheres.