Background: Since the treatments of long tracheal lesions are associated with some limitations, tissue engineered trachea is considered as an alternative option. This study aimed at preparing a composite scaffold, based on natural and synthetic materials for tracheal tissue engineering. Methods: Nine chitosan silk-based scaffolds were fabricated using three freezing rates (0.5, 1, and 2°C/min) and glutaraldehyde (GA) concentrations (0, 0.4, and 0.8 wt%). Samples were characterized, and scaffolds having mechanical properties compatible with those of human trachea and proper biodegradability were selected for chondrocyte cell seeding and subsequent biological assessments. Results: The pore sizes were highly influenced by the freezing rate and varied from 135.3×372.1 to 37.8×83.4 µm. Swelling and biodegradability behaviors were more affected by GA rather than freezing rate. Tensile strength raised from 120 kPa to 350 kPa by an increment of freezing rate and GA concentration. In addition, marked stiffening was demonstrated by increasing elastic modulus from 1.5 MPa to 12.2 MPa. Samples having 1 and 2°C/min of freezing rate and 0.8 wt% GA concentration made a non-toxic, porous structure with tensile strength and elastic modulus in the range of  human trachea, facilitating the chondrocyte proliferation. The results of 21-day cell culture indicated that glycosaminoglycans content was significantly higher for the rate of 2°C/min (12.04 µg/min) rather than the other (9.6 µg/min). Conclusion: A homogenous porous structure was created by freeze drying. This allows the fabrication of a chitosan silk scaffold cross-linked by GA for cartilage tissue regeneration with application in tracheal regeneration.