Scleractinian corals are foundational to coral reefs, vital marine ecosystems under threat from climate change. Montipora, a widely distributed reef-building genus, contributes through continuous corallum mineralization, yet polyp budding and skeleton formation processes remain elusive. This study elucidates temporal and spatial dynamics of skeletal formation and polyp budding in Montipora capricornis using high-resolution micro-computed tomography (micro-CT). We demonstrate that skeleton-canal network formation precedes polyp budding at colony margins, identifying a ‘transit area’ (volumes ~1 mm³, skeleton-to-void ratio 20-35%) within tubular canals as a pathway for polyp migration to new calices. This feature serves as a morphological budding marker, enabling visualization of polyp trajectories and growth axes. The polyp-canal system undergoes dynamic changes, including concurrent skeleton formation and dissolution. These insights establish a structural framework for biomineralization regulation and colony expansion, contributing to the development of coral growth models, and informing environmental impacts on reef-building in M. capricornis.