Microstructures of constituents and interfaces yield significant influences on the failure mechanism of adhesive joints. However, limited reports can be found concerning the micromechanical behaviours in numerical models of these joints. This work developed a refined particle-based model introducing the microscale features such as surface roughness, micro-pattern and depth of resin infiltration. Aluminium adherends with mechanical surface treatments were firstly scanned using 3D laser scanning microscope. The interfacial microstructures were then simplified into a regular pattern of triangular or trigonometric function with rational roughness thresholds based on the scanning results. Single lap shear tests using joints made of epoxy adhesive (Loctite EA 9497) and none-treated aluminium adherends were performed to provide standard testing data, which was used to calibrate the microscale parameters of particle bonds to suit the bulk and interlaminar-like properties of the adhesive. The refined numerical models were subsequently developed to examine the influences of the concerned microstructural features on the joint performance and the failure mechanism. The associated effects as well as those by adhesive thickness on the fracture energies were also discussed. The results indicate that, with decreasing the adhesive thickness, the differences of fracture strength amongst various roughness see a decline. The fracture energy increment by higher surface roughness decreases when the adhesive thickness rises. It is also found that a stronger adhesive can further magnify the improvement of joint ability from increasing the surface roughness.