Desiccation cracking of soils is of critical importance in many applications, such as industry wastes, hydraulic barriers, road embankments, and agriculture practice. This paper presented a numerical approach for modelling desiccation cracks in a thin clay layer with considering the changes in material properties during drying. Based on the micro-structure theory of clay, the swell and shrinkage behavior of clay could be explained by the swelling and shrinkage of aggregates. Therefore, an aggregates-shrinking model was proposed and its parameters were determined by matching the experimental data in literature. Then, the desiccation cracking of clay in plate shape was modeled by a three-dimensional discrete element code (PFC3D). The results obtained from the proposed numerical model had been compared with the experimental results in literature, which showed that the proposed DEM model can capture the initiation and propagation of cracks in a thin desiccated clay layer.