• Integrated single-cell and spatial transcriptomics reveals stage-specific remodeling of SuSC niches in craniosynostosis.
• SuSCs exhibit premature osteogenic commitment near the suture midline, with pre-osteoblast depletion preceding upstream SuSC loss.
• Network analysis identifies Foxa3 as a candidate regulator; its knockdown reduces mineralization in the disease background.
• Spatial communication analyses implicate meningeal fibroblasts and immune cells in modulating SuSC fate.