Hydrogels have emerged as promising biomaterials for tissue regeneration; yet, their inherent swelling can cause deformation and reduced mechanical properties, posing challenges for practical applications in biomedical engineering. Traditional methods to reduce hydrogel swelling often involve complex synthesis procedures with limited flexibility. Inspired by nature's efficient designs, we present here the approach to improve hydrogel performance using 3D printing-assisted microstructure engineering. By utilizing polymerization-induced phase separation of hydrogel from copolymerization of gelatin methacrylate and hydroxyethyl methacrylate (poly(GelMA-co-HEMA)) in the confined space during vat photopolymerization (VPP) 3D printing, we replicate the cuttlebone-like microstructure of hydrogels with enhanced mechanical properties and swelling resistance. We demonstrate here a 4-fold increase in elastic modulus compared to bulk polymerization of poly(GelMA-co-HEMA), together with improved mechanical and dimensional stability. This method offers promising opportunities for practical biomedical and tissue engineering applications, overcoming previous limitations in the design and performance.