Materials extrusion with medical biodegradable hydrogel demonstrates the potential to manufacture biocompatible scaffolds in regenerative medicine. However, the unpredictable geometric change of fabricated models, such as swelling or shrinking, slower the development of complex hydrogel 3D architectures for in-vitro-functionalized tissues and organs. Inappropriate value of humidity throughout the 3D printing process is a primary reason of wrinkle or even collapse of proposed architectures. Therefore, there is a need to investigate the swelling-shrinking behavior with varying ambient humidity and to search for the appropriate value of humidity in hydrogel printing process. This study established a thermal-humidity-multiphase flow coupling field simulation model for investigating the humidity-driven swelling-shrinking behavior of hydrogel filaments numerically. Subsequently, the appropriate value of 3D printing humidity for hydrogel filaments with diameters of 0.2 mm, 0.3 mm, and 0.4 mm were explored, which were respectively set to 90%, 80%, and 60%. Furthermore, groups of structures were fabricated with the selected humidity, which demonstrated a moderated moisture loss of 3D architecture. A human ear model was successfully manufactured, of which the effective size reached 20 mm(length) × 10 mm (width) × 10 mm(height).