The effect of glutaraldehyde and calcium cations as covalent and ionic crosslinkers was investigated on the main characteristics of scaffolds based on chitosan and cellulose nanocrystals. Therefore, four different scaffolds based on chitosan/cellulose nanocrystals with different crosslinking methods were fabricated using the freeze-drying method for potential use in bone tissue engineering. The structural and chemical features of prepared scaffolds were studied by the FTIR technique. FESEM images revealed that all scaffold samples are porous three-dimensional networks in which the pores are connected. TGA analysis showed that the thermal stability of scaffolds based on chitosan/cellulose nanocrystals has not been changed significantly by using different crosslinking methods. The chitosan/cellulose nanocrystals scaffold crosslinked by glutaraldehyde represented the highest compressive strength and the uncrosslinked scaffold showed the highest swelling ratio in comparison to the other scaffolds. The fastest degradation rate belonged to the scaffold crosslinked by calcium cations. FESEM images and EDX analysis confirmed that fabricated scaffolds have good biomineralization ability. The cell viability and cell attachment results indicated that all four scaffolds support cell proliferation and cell adhesion. However, the viability of NIH3T3 fibroblast cells in the presence of glutaraldehyde-containing scaffolds was lower than that of other scaffolds.