The choroid plexues in the zebrafish hindbrain controls the exchange of substances between brain and its vessels,and the vascular abnormalities around the choroid plexues can lead to associated cerebrovascular diseases. We first performedserial imaging of the major blood vessels in the hindbrain region of zebrafish, and obtained a series of images of zebrafish between 43 hours and 63 hours after fertilization using confocal microscopy to photograph embryos under normal conditions andafter cylindrospermopsin treatment. Afterwards, the DE-3D U-Net was developed for the segmentation of the hindbrain images.The segmentation results showed that the class pixel accuracy of DE-3D U-Net could reach to 86.67%, 93.18% and 83.74% forthe three main vessels and the segmentation results were used to plot vascularization curves. The quantitative results showed thatthe radii of the three vessels showed a reduction of 18% after treatment with high concentrations of cylindrospermopsin, and theangle of the mesencephalic vein showed a reduction of 30° to 50°. This study proposed a neural network for segmentation ofhindbrain vessels of zebrafish, and it provided a basis for research on the development of zebrafish choroid plexsus.