This paper presents a new approach for the modelling of heat transfer in 3D discrete particle systems. Using a combined finite–discrete element (FDEM) method, the surface of contact is numerically computed when two discrete meshes of two solids experience a small overlap. Incoming heat flux and heat conduction inside and between solid bodies are linked. In traditional FEM (finite element method) or DEM (discrete element method) approaches, to model heat transfer across contacting bodies, the surface of contact is not directly reconstructed. The approach adopted here uses the number of surface elements from the penetrating boundary meshes to form a polygon of the intersection, resulting in a significant decrease in the mesh dependency of the method. Moreover, this new method is suitable for any sizes or shapes making up the particle system, and heat distribution across particles is an inherent feature of the model. This FDEM approach is validated against two models: a FEM model and a DEM pipe network model. In addition, a multi-particle heat transfer contact problem of complex-shaped particles is presented.