To address problems such as the lack of accuracy in acquiring depth maps for dynamic fish 3D measurements by usual binocular vision or a time-of-flight (TOF) depth camera, a TOF-assisted binocular vision depth acquisition algorithm is used to obtain high-quality depth maps. The TOF depth energy function is designed to guide the binocular stereo matching process, which improves the correct matching rate of binocular matching in low-texture regions; the TOF and binocular stereo matching confidence weighting functions are designed to achieve the fusion of the two at pixel level to improve the matching quality of fish in the occluded overlapping regions. The experimental results show that the TOF-assisted binocular vision system improves the accuracy of fish size measurement compared to single binocular vision while reducing the measurement error when the fish body has a significant inclination along the depth axis.