Objective We propose a dual-contrast optical projection tomography (DC-OPT) based on principal component analysis (PCA) to obtain a three-dimensional (3D) visualization of the blood-flow network and skeleton in a live organism.Methods The PCA method was used to extract the absorption and flow contrast images (15 images/projection position). The absorption image was obtained with the use of the first principal component of the raw image sequence. The flow images were obtained based on the computation of the modulation depth of each pixel. The flow and absorption contrast images at different projection positions are combined to achieve a synchronous reconstruction of a 3D image.Results The combination of PCA and OPT is used to realize the 3D imaging of the blood-flow network and skeleton of the biological sample by separating the dynamic blood flow signal and the static background signal of the sample.Conclusion The novelty of our study is attributed to the fast, simultaneous, dual-contrast 3D images of the blood-flow network and skeleton by the same optical system. The experimental result can be applied in physiological development studies in live model organisms.