The effects of microstructure on diffusion behaviors of Ni in Zr48Cu36Ag8Al8 alloy were investigated by transmission electron microscope and secondary ion mass spectrum. The temperature dependence of Ni diffusivities in Zr48Cu36Ag8Al8 alloy with different states (metallic glass, nanocrystals and coarse crystals) has been measured in the temperature range of 693–723 K. The results show that diffusion behavior is microstructure dependence, and the relations between the microstructure and diffusion are discussed. The activity energy of the grain boundary diffusion in nanocrystals calculated by the Suzuoka solution is about 1.433 eV/atom. It is equivalent with that of metallic glass, which is attributed to the similar microstructure between the two. Copyright © 2016 John Wiley & Sons, Ltd.