Abstract Nanotwinned Al/Ti multilayers have exhibited size-dependent microstructure evolution and high strength. However, their deformation mechanisms are less well understood. In this work, we investigated the deformation mechanisms of nanotwinned Al/Ti multilayers with FCC/HCP layer interfaces by using in situ micropillar compression tests. Nanotwinned Al/Ti multilayers exhibit compressive strength up to 2.4 GPa and good work hardening capability. Post-compression TEM analyses reveal high-density stacking faults and the HCP-to-FCC phase transformations in Ti. Molecular dynamics simulations elucidate the mechanisms of deformation induced phase transformation in Ti and the influence of collective movement of partial dislocations on the deformability of Al/Ti multilayers.