Autoregulation of nodulation is a long-distance shoot-root signalling regulatory system that regulates nodule meristem proliferation in legume plants. However, due to the intricacy and subtleness of the signalling nature in plants, molecular and biochemical details underlying mechanisms of autoregulation of nodulation remain largely unknown. The purpose of this study is to use functional-structural plant modelling to investigate the complexity of this signalling system. There are two major challenges to be met: modelling the 3D architecture of legume roots with nodulation and co-ordinating signalling-developmental processes with various rates.Soybean (Glycine max) was chosen as the target legume. Its root system was observed to capture lateral root branching and nodule distribution patterns. L-studio, a software tool supporting context-sensitive L-system modelling, was used for the construction of the architectural model and integration with the internal signalling.A branching pattern with regular radial angles was found between soybean lateral roots, from which a root mapping method was developed to characterize the laterals. Nodules were mapped based on 'nodulation section' to reveal nodule distribution. A root elongation algorithm was then developed for simulation of root development. Based on the use of standard sub-modules, a synchronization algorithm was developed to co-ordinate multi-rate signalling and developmental processes.The modelling methods developed here not only allow recreation of legume root architecture with lateral branching and nodulation details, but also enable parameterization of internal signalling to produce different regulation results. This provides the basis for using virtual experiments to help in investigating the signalling mechanisms at work.