The architecture of hydrogel composites results in not only synergistic property enhancement but also superior functionality. The reaction−diffusion (RD) process is acommon phenomenon throughout nature which induced ordered structure on a length scale from microscopic to macroscopic. Different from commonly used inorganic salts or oppositely charged nanoparticles for the RD process, a modified RD process was used for layered chitosan hydrogel (L-CH) and layered magnetic chitosan hydrogel (L-MCH). During the modified RD process reported in this paper, the protonated chitosan (CS-NH3+) with iron ions (Fe3+ and Fe2+) was used as an inner-reactant and hydroxide ion (-OH−) was used as an out-reactant. The protonated chitosan (CS-NH3+) not only played the role of an inner-reactant but also the reaction medium which controlled the diffusion behavior of the out-reactant (-OH−). A series of ordered layers were constructed and the ordered layers were parallel with the longitudinal axis. The layer width of L-CH and L-MCH can be tailored by varying interval time T. The mean layer width of L-MCH increased from 50 ± 5.8 μm to 90 ± 6.4 μm when the interval time T increased from 2 min to 5 min. The tailored layer structure of L-CH and L-MCH obeyed the time law and spacing law, which declared that the L-CH and L-MCH were constructed via the reaction−diffusion process. We also show that the tailored layer structure endows hydrogel with enhanced mechanical properties, especially toughness. The yield strength of magnetic chitosan hydrogel was improved significantly (from 95.1 ± 7.6 kPa to 401.7 ± 12.1 kPa, improved by about 4 times) when 10 wt. % magnetite nanoparticles were involved. The enhancement of the mechanical propertieswas due to a physical crosslinking effect of magnetite nanoparticles on chitosan. For L-MCH, the probe displacement reached 28.93 ± 2.6 mm when the rupture occurred, which was as high as 284.7% compared with that of the non-layered hydrogel. The tailor-made hydrogels might be possible for application as a tough implantable scaffold.