The invention discloses an opto-acoustic tomography reconstruction method based on a frequency domain and a wave number field. The method comprises the following steps: acquiring radio frequency dataand system parameters, performing time gain compensation, performing three-dimensional Fourier transform, performing interpolation processing, performing three-dimensional Fourier transform, performing demodulation to obtain envelope, adjusting a contrast ratio, outputting opto-acoustic images, and optimizing the opto-acoustic images. By adopting the method, three-dimensional reconstruction on opto-acoustic signals is implemented in a frequency domain and a wave number field, the influence that signals are not completely acquired in a limited angle can be reduced, and meanwhile, the influenceof nonuniformity of sound velocities is taken into account. The reconstruction method disclosed by the invention has the advantages of being high in reconstruction image resolution, high in signal tonoise ratio, small in fake shadow and rapid in reconstruction calculation speed.