Abstract: An endoscopic Doppler OCT system based on swept-source optical coherence tomography (SS-OCT) and phase-resolved Doppler algorithms was constructed in the study, and an endoscopic probe based on GRIN lenses and MEMS micromirrors was used to realize the measurement of flow rate information. After performance testing, the axial resolution of the system was obtained to be 6.88 μm, the lateral resolution was 15.79 μm, and the imaging depth was about 3.4 mm; the system could realize an imaging speed of 50 frames/s when outputting a 2D image of 1000×1024 size. Simulation experiments of flow rate measurement using agar and capillary glass tubes were carried out, and it was verified that the system constructed in this paper could obtain the flow rate distribution of the cross-section under test, and the measured distribution was basically consistent with the theory. The syringe pump was set to perform experiments at different flow rates, and the measured average flow rate values were basically consistent with the set values within the error range. The results show that the endoscopic Doppler OCT system based on MEMS micromirror designed in this paper can well meet the needs of laminar imaging and flow velocity detection.