Recent studies on autophagy demonstrated a new extracellular secretion pathway for autophagosomes in addition to the routinely described intracellular degradation pathway. Besides, the secretory autophagosomes were found closely related to the occurrence and development of cancers. Therefore, analysis of the protein expression on secretory autophagosomes is a promising noninvasive strategy for cancer diagnosis and mechanism study. Herein, we constructed a three-dimensional (3D) microfluidic chip employing a fusiform micropillar array and layer-by-layer modification of gelatins, which obviously enhanced the mass transfer between reactants and increased the immobilization sites for capture antibody. As a result, the autophagosome capture efficiency of the 3D chip (74%) is significantly higher than that of the unmodified flat chip (47%). Using a two-step immunoreaction, ovarian cancer cell-secreted autophagosomes were successfully captured and detected. The results showed that two proteins, LC3B and HSP60 at the surface of autophagosomes, can be detected with limits of detection (LODs) of 141 particles μL-1 and 126 particles μL-1, respectively. In addition, both LC3B and HSP60 expressions on autophagosomes can be used to distinguish the serum samples between cancer patients and healthy people, with a p value less than 0.01 (statistically significant difference) or 0.05 (statistically different), respectively. Moreover, the summed signal of LC3B and HSP60 showed a p value less than 0.001 (extremely statistically significant difference), demonstrating the good potential of this chip for further application in cancer diagnosis.