The light-sheet flow imaging system (LS-FIS) enables high-resolution, high-throughput three-dimensional imaging of miniature model organisms like zebrafish. This capability presents potentially broad application prospects in the fields of developmental biology and drug screening. To study correlations between zebrafish structures, this study expanded on the original monochromatic LS-FIS to enable dual-color fluorescence imaging. To calibrate the resolution of the dual fluorescent channels, fluorescent microspheres were employed. Registration of dual-channel images and reconstruction of three-dimensional volumes were achieved using scale-invariant feature transform (SIFT) in combination with the random sample consensus (RANSAC) algorithm. Subsequently, this system was used to perform simultaneous imaging of zebrafish vasculatures and erythrocytes. Three-dimensional images were obtained and analyzed, revealing the distribution of vasculatures and erythrocytes in zebrafish larvae at 4 and 9 days post-fertilization.