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Velocity measurement of an intermittent high-speed flow inside a micro wave rotor cell was carried out using a laser Doppler anemometry (LDA). The cell is 3 × 3 mm rectangular tube, whose length is 42 mm. The pressure ratio and rotor speed of the wave rotor were set at 2.5 and 5,000 rpm, respectively. Ethanol droplets were seeded into the flow as scattering particles. By use of laser beam expanders, the probe volume of the LDA optics was minimized, and sub-millimeter special resolution is realized while a wide velocity range (-100 to 300 m/s) is kept. It is shown that the velocity histories at local positions inside the wave rotor cell can be obtained with the LDA optics. The rapid velocity increase and decrease, due to the primary and secondary shock waves, are observed, and the propagation speed of the shock waves was estimated. It is shown that the velocity profile inside the cell is flat and that the boundary layer thickness inside the cell is smaller than 0.5 mm.