Following DPST crosslinking of human neuroblastoma cells, nuclear-cytoplasmic fractionation was performed using hypotonic lysis to obtain cytoplasmic and nuclear protein compartments. Through systematic analysis of crosslinking mass spectrometry data, we elucidated how subcellular compartmentalized microenvironments regulate spatial distribution of protein conformations and topological architecture of interaction networks. This study reveals the heterogeneous principles governing dynamic protein assembly between nuclear and cytoplasmic compartments in neuroblastoma cells.