The invention belongs to the bioanalysis technical field, and relates to a rotational scanning capillary array analyzer. The analyzer comprises a laser light source, a scanning reflector, a scanning objective, a detection window fixing device, a capillary sampling end, a capillary exhaust liquid end, a light beam steering system, a fluorescence spectroscope, a fluorescence color filter, an optical detector and a scanning central shaft, wherein, a plurality of capillaries are arranged around the scanning central shaft to form a cylindrical array, and the capillary array is fixedly arranged in the detection window fixing device; laser beam of the light source sequentially passes through the fluorescence spectroscope, the scanning reflector, the light beam steering system and the scanning objective, and the scanning objective converges the laser beam on the detection window; a biological sample marked with fluorescence in the capillary is activated by the laser, irradiated fluorescence passes through the scanning objective, the light beam steering system, the fluorescence spectroscope and the fluorescence color filter, and is detected by the optical detector. The rotational scanning capillary array analyzer has the advantages of high flux, high sensitivity, large fluorescence collection angle and good performance.