The invention relates to the technical field of biomedicine, and provides a blood separation device based on acoustic fluid mechanics. The blood separation device comprises a micro-fluidic chip, a micro-fluidic pump and a sound wave driving system, wherein the micro-fluidic pump is connected with the micro-flow channel of the micro-fluidic chip through a hose, micropores distributed in an array mode are formed in the bottom face of the micro-flow channel, the piezoelectric transducer of the sound wave driving system is fixed to the glass substrate of the micro-fluidic chip, microfluid enters the micro-flow channel under the action of the micro-fluidic pump, particles in the microfluid are separated according to different acoustic flow field forces borne by the particles with different particle sizes in an acoustic flow field, and by controlling the acoustic flow capture force borne by the particles and the thrust of an external flow field, the particles with relatively large particle sizes are captured by the micropores, and the particles with relatively small particle sizes migrate along with the flow field. According to the blood separation device, particles in blood are not damaged, the controllability is high, and target bacteria can be simply and efficiently separated from the blood.