Unlike crystalline metals, which have a well-understood periodical structure, the amorphous structure of metallic glasses (MGs) is still poorly understood, particularly when such a structure rearranges itself at the nanoscale under external agitations. In this article, we provide compelling evidence obtained from a recently developed high-resolution atomic force microscopy (HRAFM) technique that reveals the nanoscale structural heterogeneity after thermal annealing in a Zr–Ni metallic glass. Through the HRAFM technique, we are able to uncover the annealing-induced fractal growth of the dense-packing phases in the binary MG thin film, which exhibits a fractal dimension of ∼1.7, in line with a two-dimensional diffusion limited aggregation process. The current findings not only reveal the evolution process of atomic packing in the annealed MG thin film, but also shed light on the possible cooling rate effect on the atomic structure of MGs.