Serious spinal cord injury (SCI) often leads to disorganized axon regeneration, impeding the accurate projection of neural signals. This study aims to rebuild spinal tracts by targeting the collagen VI (COL6)-induced axonal fasciculation pathway, which is active during spinal cord development but diminishes in regenerating spinal cord. A thiol-modified hyaluronic acid hydrogel crosslinked with COL6 (HAPC) is proposed to reactivate spinal tract morphogenesis for regeneration. Neurites cultured on the HAPC substrate exhibited a straight-bundled pattern, contrasting with the straggly pattern observed in control groups that lacked COL6. The dynamics of axonal aggregation and proximal retraction are determined to drive the formation of straight axon bundles. Experiments on a rat spinal cord transection model demonstrates that treatment with HAPC significantly induces the organization of spinal tract-like structures and promotes the targeted projection of 5-Hydroxytryptamine (5-HT) axons, along with improved functional recovery. These findings highlight the role of COL6 in spinal tract self-organization and the potential of HAPC for treating clinical SCI.