The rejuvenated metallic glasses subjected to heat treatments show the improved thermal stability and properties. The atomic structure in the glassy alloys inherited from the liquid state possesses the medium-range order that could be significantly modified upon heating. In this work, we utilized the nano-beam diffraction technique to resolve the medium-range order in a glassy Ti-Ta-based surface alloy upon isothermal annealing. After annealing at T = 773 K the as-received Ti-Ni-Ta surface alloy, fabricated by a liquid-phase mixing of the system [Ti-Ta film/TiNi substrate], devitrified through the formation of a nanocrystalline structure: η′-(Ti,Ta)2Ni + β(Ti,Ta) + α″(Ti,Ta). The transmission electron microscopy methods were employed to determine the parameters of the short-range order in the amorphous phase both in the reciprocal and real spaces. For interpretation of the results of the electron scattering in the reciprocal space, the coherent and diffuse scattering intensities were calculated in the framework of the multi-shell cluster model. We suggested a scheme describing the transformations of icosahedral nanoclusters during the temperature-induced rejuvenation. A methodology on the selection of the validated two-shell cluster model reproducing the medium-range order was proposed.