Root system architecture (RSA) refers to the geometric features and topology of the root system. Ground-penetrating radar (GPR) is a possible method of RSA reconstruction. However, because the topology of the root system is not directly accessible by GPR, GPR-based reconstruction must be complemented by manual connection of root points, resulting in limited accuracy. In this study, we used both GPR and direct excavation to obtain 3D coordinates (XYZ coordinates) and diameters of moso bamboo rhizomes on an orthogonal grid. A score function for selecting the best-connected root points was developed using rhizome diameter, depth, extension angle, and measured line spacing, which was then used to recover the topology of discrete root points. Based on the recovered topology, the 3D RSA of the rhizomes was reconstructed using a smoothing function. Based on the excavation data, the reconstructed RSA was generally consistent with the measured RSA, with 78.13% of root points correctly connected. The reconstructed RSA based on GPR data thus provided a rough approximation of the measured RSA, with errors arising due to missing root points and rhizome displacement. The proposed algorithm for reconstructing 3D RSA further enriches the application of ground-penetrating radar to root detection.