Objective To explore an easy to perform three-dimensional reconstruction method based on serial section images of large tissue by combination of several new techniques. Methods After the processes of HE stain, digitalization, assembling and alignment, the digitalized image database of long serial sections from a normal rat renal paraffin-embedded tissue was made, in which the vascular system and pelvis were segmented and reconstructed, the morphology figures of constructed result were also measured. Results The image database composed of clear whole images and correct registration reappeared structural pattern of the tissue, and the results displayed the complicated positional relationship of renal structures and could be observed freely, some three dimensional figures including percentage components of kidney, length and angel of arteries were obtained. Conclusion We reported a three-dimensional reconstruction method from serial sections with accepting results. It can also be used in other cases needing stereoscopic information or intuitive observation.