To better understand the factors determining the multi-step relaxation processes in polynuclear lanthanide single molecule magnets (SMMs), two Dy(iii)4 SMMs showing two-step relaxation processes were elaborately designed and investigated for their structure-dependent magnetic properties. Through targetedly fine-tuning the auxiliary ligand (from the anion of 1-phenylbutane-1,3-dione to 2-acetylcyclopentanone) on specific Dy(iii) sites while retaining the same type of coordination atoms, one of the two relaxation processes shifted to higher temperature with an increase of energy barrier, which permits the unambiguous assignment of the relaxation processes to specific metal sites. Therefore, the present {Dy4} systems provide a good example to probe the factors determining the relaxation dynamics, and point to a simple way to optimize the magnetic performance of polynuclear dysprosium SMMs.