For the purpose of controlling zeolite crystal size, crystallization of zeolite NaA and NaY in glutaraldehyde crosslinked chitosan (GA-CS) hydrogels was studied in this paper. The zeolite crystals were produced by penetration of Na2O–Al2O3–H2O alkaline solution into GA-CS hydrogels filled with colloidal silica, followed by hydrothermal treatment and removal of GA-CS hydrogels. We systematically investigated the effects of the synthesis parameters – including the amounts of silica, chitosan, and glutaraldehyde, and the aging and heating times – on the size, size distribution and crystallinity of the particles. A hydrogen peroxide treatment method was shown to be an effective way for removing GA-CS hydrogels, thereby avoiding the conventional calcination step. X-ray diffraction (XRD), light scattering, scanning electron microscopy (SEM), thermogravimetric analysis (TG), and N2 sorption were used to characterize the zeolite samples. This work showed that GA-CS is a promising space-confinement medium for the synthesis of zeolite nanocrystals with tunable crystal sizes and excellent dispersibility.