A dinuclear dysprosium cluster [Dy2(NO3)4(H2O)2(L)2]·2CH3CN was successfully prepared by employing HL (HL = 2,6-dimethoxyphenol) and Dy(NO3)3·6H2O in a mixture of CH3OH and CH3CN. The conversion of this Dy2 compound by reaction with additional deprotonated ligand generated a Dy9 cluster [Dy9(μ4-OH)2(μ3-OH)8(μ2-OCH3)4(NO3)8(H2O)8(L)4](OH)·2H2O with the well-known "diabolo" topology. Magnetic investigation revealed that both of the clusters exhibit typical SMM characteristics, and variable magnetic relaxation with the energy barrier changing from 217.87 K to 9.24 K along with the transition from a dinuclear dysprosium cluster to a nonanuclear one. Ab initio calculations further confirm the corresponding structure-activity relationships that originate the different magnetic behaviours. This design may afford a feasible strategy for modulating the magnetic relaxation dynamics of polynuclear systems.