Exosomes are considered promising indicators for early cancer diagnosis. The multiple protein biomarkers carried by exosomes are associated with diverse significant biological processes and are important biomarkers of cancer subtypes. However, it is challenging to sensitively and accurately quantify protein biomarkers from a few exosomes. Herein, we propose an ultrasensitive method for quantitatively profiling protein biomarkers on the surface of exosomes by integrating mass spectrometry imaging and gold nanoparticle (AuNP)-based signal amplification. Organic oligomers as mass tags and specific antibodies are modified on AuNPs to form biomarker probes. Exosomes captured by the antibody-coated gold chip are recognized by the AuNPs probes, forming a sandwich immunoassay. By mass spectrometry imaging the mass tags, multiple protein biomarkers can be quantitatively detected from the exosomes, with a limit-of-detection (LOD) down to 50 exosome particles. As a proof of concept, exosomes secreted by different breast-cancer cell subtypes, i.e. MCF-7 and MDA-MB231, were distinguished by the level of surface protein biomarkers of CD9, CD44, and epithelial cell adhesion molecule (EpCAM) acquired by the method, demonstrating that exosomes could be used for the diagnosis of cancer at subtype level. In consideration of the advantages of the ultrasensitivity, accuracy, and simplicity, the strategy has potential prospects in biomarker discovery, cellular phenotype characterization, and cancer diagnosis.