A large-scale molecular dynamics (MD) simulation of nano-indentation was carried out to provide insight into the influence of the Al-AlO interface on dislocation evolution and deformation behavior of Al substrate coated with AlO thin film. Adaptive common neighbor analysis (a-CNA), centro-symmetry parameter (CSP) estimation, and dislocation extraction algorithm (DXA) were implemented to represent structural evolution during nano-indentation deformation. The absence of elastic regime was observed in the P-h curve for this simulated nano-indentation test of AlO thin film coated Al specimen. The displacement of oxygen atoms from AlO to Al partly through the interface greatly influences the plastic deformation behavior of the specimen during nano-indentation. Prismatic dislocation loops, which are formed due to pinning of Shockley partials (1/6 < 112>) by Stair-rod (1/6 < 110>) and Hirth dislocation (1/3 < 001>), were observed in all cases studied in this work. Pile-up of atoms was also observed and the extent of the pile-up was found to vary with the test temperature. A distorted stacking fault tetrahedron (SFT) is formed when a nano-indentation test is carried out at 100 K. The presence of a prismatic dislocation loop, SFT and dislocation forest caused strain hardening and, consequently, there is an increase in hardness as indentation depth increases. Graphical abstract Figure illustrates nano-indentation model set up along with load vs. depth curve and distorted stacking fault tetrahedron.