Exosomes play a crucial role in cancer formation and metastasis which are regarded as a prospective target to cancer diagnosis in liquid biopsy. However, researches about isolating and detecting exosomes remain tardy because of the morphology limitations of exosomes. Here we present an integrated on-chip isolation and analysis system for exosome tumor marker detection. Exosomes were isolated with magnetic beads and labelled by quantum dot (QD) probes in the isolation zone, then the exosome-labelled magnetic beads queued uniformly among the micropillar arrays in the analysis zone. Fluorescence intensity detection in our system was performed by measuring and averaging the fluorescence intensity of each single bead, thus experiment results could be more accurate. Fabrication of the chip was simple and low-cost. These advantages certify our system to be a potential non-invasive method for exosome marker detection and cancer diagnosis.