Synthetic hydrogels possessing both macroscopic anisotropic structure and toughness, which are analogous to the load-bearing bio-tissues such as muscles and tendons, are rarely available. Studying the molecular mechanism of tough and anisotropic hydrogel under deformation is beneficial to understand the load-deformation functions of soft bio-tissues. In this work, the deformation-induced structure transformation of a macroscopically anisotropic and tough hydrogel has been investigated to understand the role of structure evolution for enhanced toughness. At rest, the hydrogel possesses a well-defined hierarchical structure in which self-assembled nanometer thick lamellar bilayers are alternatively stacked in hundred nanometer thick hydrogel matrixes. Stretching along the lamellar direction induces structure transformation from lamellar bilayers to hierarchical fibrous structures aligned along the deformation axis. The generated hierarchical structures consist of micrometer thick fiber bundles made from nanometer thick fibrils analogous to tropo-collagen bundles or microfibrils of the tendon. The fibrous structure formed at large elongation is associated with damage and rupture of the bilayers, which underpins the molecular mechanism of the unique mechanical behaviors of the tough lamellar hydrogel.