Discrete element (DE) model has a great feasibility in modelling the microstructural behaviours of adhesive composite joints. However, it demands a sophisticated calibration process to determine microscale bond parameters, which involves massive efforts in both experimental and numerical investigations. This work developed a novel calibration strategy based on DE models and genetic expression programming (GEP) approach for predicting the behaviours of hybrid composite joints encompassing the material nonlinearity, large ductile deformation and multiple fracture modes. In the developed strategy, both the bulk and interlaminar-like properties of ductile adhesives were concerned to suit various joint configurations. GEP modelling was performed based on the datasets from virtual DE experiments. Symbolic regression models were subsequently developed to facilitate the parameters determination. A series lab tests were conducted to validate the numerical results. It shows that the calibrated DE model can adaptively simulate the featured behaviours of both the ductile adhesive and composite joints with different configurations well in most examined occasions. Therefore, it could be suggested to generalize the developed strategy in the development of other DE models for saving the massive efforts in the calibration process of microstructural parameters.