Classical molecular dynamics simulation is used for structural thermodynamic analysis of Ni-Ti bimetallic clusters. Experimental observation for the nanoclusters synthesized by the bioreduction method is used to consolidate the conclusion. The results demonstrate that Ni-Ti nanoclusters as small as 2-3 nm are not energetically favorable for common ordered geometrical arrangements such as cuboctahedron, decahedron, and icosahedron, though they can be synthesized experimentally. For the elemental distribution, Ni and Ti tend to aggregate separately. In the cases under study, eutectic-like and Ni-core/Ti-shell structures can keep their basic shape and elemental distribution during long periods of relaxation at room temperature. For other cases such as solid solution and Ti-core/Ni-shell, the structures amorphized and the elements tend to distribute uniformly even though they are at temperatures as low as room temperature. Experimental evidence was obtained by the analysis of biosynthesized nanoparticles using transmission electron microscopy techniques. This allowed determination of the partial amorphized structures of small bimetallic particles with cubic and multiple twined-like structures.