This article focused on the microstructure changes of the Zirconium-based alloy with isothermal annealing close to the glass transition temperature. The differential scanning calorimetry (DSC) was used to measure the temperatures of crystallization and glass transition. The Small-angle neutron scattering (SANS) results revealed a peak associated with the interference in isothermal annealing. Under supercooling, crystallization was decomposed, in addition to transmission electron microscopy (TEM) results exhibited that a part of inhomogeneities formed at the early annealing of amorphous alloy had been crystallized later. TEM and x-ray diffraction (XRD) results illustrated that nanocrystalline phase formed after long time annealing, with decomposition of the initial phase. Nanoindentation experiments showed that the hardness descended on the increase of indentation loaded, while the excessive free-volume increased with the increasing indentation load.