In legume plants, the balance of nodule formation is maintained by a long-distance shoot-root signalling system known as autoregulation of nodulation. Due to the complexity of plants’ signalling nature, the underlying mechanisms of autoregulation of nodulation still remain largely unknown. The purpose of our research is to use functional-structural plant modelling to help in further investigating this regulatory system. For such a purpose, there are two major challenges to be met: modelling the 3D architecture of legume roots and coordinating signalling-development processes with various rates. Using soybean as the target plant and L-studio as the modelling platform, we have developed a series of methods and techniques to collect root development data, reconstruct root architecture, and synchronise the multi-rate signalling and developmental events. These methods and techniques may also be applicable to studies on lateral root initiation and relevant regulations.