Clarification of root morphology is important for understanding tree root functions. A 3D laser scanner reconstructs the 3D structure of root system with high accuracy, but the devices are large and expensive. The Structure-from-Motion (SfM) method reconstructs the 3D structure of an object from multiple images. This method has high applicability including field research because it acquires the 3D data from 2D images with a commercially available digital camera. Our aim in this study was therefore to develop an efficient method using SfM for morphological measurement of whole tree root systems. The 3D root system model was created using three black pine root systems. A series of image data was collected from the root systems using a camera and reconstructed using the free software, VisualSfM and MeshLab. We evaluated the accuracy of morphological data estimated from the 3D models by comparing them with real data obtained from manual measurements. The 3D reconstructions of the root systems were successful. The root mean squared error values for the morphological features in the root systems ranged from 4 to 24%, which was sufficiently accurate for the 3D model. We also report the possible errors of 3D reconstruction of tree root systems using SfM.