This study introduces a novel method called Cross-link Assisted Spatial Proteomics (CLASP) to map sub-organelle proteomes and membrane protein topologies. CLASP leverages cross-linking mass spectrometry (XL-MS) to achieve high-resolution spatial proteomics, addressing the limitations of existing methods such as APEX/BioID and proximity labeling approaches. Using human mitochondria as a model, the authors demonstrate that CLASP can elucidate the spatial proteomes of all mitochondrial sub-compartments and provide insights into membrane protein topology. Biochemical and imaging studies validate the accuracy of CLASP, confirming the discovery of mitochondria-associated proteins and revising previous protein localization data. The method is also validated in synaptic vesicles, showing its applicability to different sub-cellular compartments. CLASP extends the scope of XL-MS beyond structural biology and interactomics, enabling systematic profiling of sub-organelle and membrane proteomes. The study establishes CLASP as a powerful tool for spatial proteomics, offering high-resolution spatial information and facilitating biological discoveries.This study introduces a novel method called Cross-link Assisted Spatial Proteomics (CLASP) to map sub-organelle proteomes and membrane protein topologies. CLASP leverages cross-linking mass spectrometry (XL-MS) to achieve high-resolution spatial proteomics, addressing the limitations of existing methods such as APEX/BioID and proximity labeling approaches. Using human mitochondria as a model, the authors demonstrate that CLASP can elucidate the spatial proteomes of all mitochondrial sub-compartments and provide insights into membrane protein topology. Biochemical and imaging studies validate the accuracy of CLASP, confirming the discovery of mitochondria-associated proteins and revising previous protein localization data. The method is also validated in synaptic vesicles, showing its applicability to different sub-cellular compartments. CLASP extends the scope of XL-MS beyond structural biology and interactomics, enabling systematic profiling of sub-organelle and membrane proteomes. The study establishes CLASP as a powerful tool for spatial proteomics, offering high-resolution spatial information and facilitating biological discoveries.