This paper presents a novel coupled model of discrete element method (DEM) and finite difference method (FDM) to investigate the load-deformation of stone columns reinforced soft clay. In the proposed model, the soft clay domain was modelled by the continuum method using FLAC and stone column was modelled by the discrete element method using PFC2D. Algorithms and mathematical framework to assist coupling between the two domains were introduced, in which the DEM transfers forces and moment to the FDM and then the FDM provides an update of displacements to the DEM. The predicted load-deformation responses obtained from the coupling model reasonably agreed well with data measured experimentally, indicating that the proposed coupling discrete-continuum model could capture the deformation behavior of stone column stabilized soft clay. Evolutions of contact force distributions developed in stone column at varying levels of settlement were presented. Shear stress-strain contours induced in the surrounding soft soils were also investigated.