Nuclear pore complex (NPCs) is the largest non-polymeric protein complex in the cell. It mediates nucleocytoplasmic transport. The intricate 120 MDa architecture remains incompletely understood. We combine AI-based structure prediction with in situ and in cellulo cryo-electron tomography and integrative modeling to report near complete model of human NPC scaffold. We show that linker Nups spatially organize the scaffold within and across subcomplexes to establish the higher-order structure. This work exemplifies how AI-based modeling can be integrated with in situ structural biology to understand subcellular architecture across spatial organization levels.