In this paper, a multi-exposure fusion high-motion projection tomography three-dimensional imaging method based on spatial frequency filtering is proposed to realize the three-dimensional structure imaging of living zebrafish(17 mm×4 mm, maximum thickness 2.33 mm, minimum thickness 0.29 mm). Our method is to record the series of absorption images by using different exposure time of the camera, transform each image into the frequency domain to remove the low frequency, and then superimpose each filtered spatial frequency signal and inverse Fourier transform back into the air domain, and the transformed image is normalized to obtain a high dynamic image. The high dynamic absorption projection image is obtained at each projection angle, and then reconstructed by a filtered back projection algorithm to obtain highly dynamic three-dimensional structure information. The experimental imaging results show that the multi-exposure fusion high-visibility optical projection tomography three-dimensional imaging study of spatial frequency filtering can obtain more abundant spatial information of complex structures, and the relationship and process of early embryo growth and development of zebrafish monitoring and quantitative assessment have certain application prospects.