A method and apparatus for washing solid substrate with ultrasonic wave after hybridization reaction are provided. The method includes (1) putting the solid substrate into a container having a washing solution, on which the hybridization reaction has been completed, (2) using an ultrasonic generator to produce a certain strength of ultrasonic wave and transmit it into the washing solution, (3) washing the substrate by means of the cavitation effect being produced in the washing solution by the ultrasonic wave. Since the cavitation bubbles in the washing solution can produce intensive efflux and local microslipstream against the solid surface, evidently reducing the liquid surface tension and friction and enhance the liquid flow, non-specific adsorbate and deposit bound weakly on the solid substrate can be washed down rapidly.