Intermetallic NixMy (M = Ga and Sn) nanocrystals with uniform particle size and controlled composition are successfully synthesized via a solution-based co-reduction strategy. The as-obtained nanocrystals are crystalline and structurally ordered. The active-site isolation and modified electronic structure are responsible for the excellent catalytic performance for alkyne semi-hydrogenation of the as-obtained non-precious catalysts.