The spin-dependent electron transport in the ferrocene-based molecular junctions, in which the molecules are 1,3-substituted and 1,3′-substituted ethynyl ferrocenes, respectively, is studied by the theoretical simulation with nonequilibrium Green’s function and density functional theory. The calculated results suggest that the substitution position of the terminal ethynyl groups has a great effect on the spin-dependent current-voltage properties and the spin filtering efficiency of the molecular junctions. At the lower bias, high spin filtering efficiency is found in 1,3′-substituted ethynyl ferrocene junction, which suggests that the spin filtering efficiency is also dependent on the bias voltage. The different spin-dependent transport properties for the two molecular junctions originate from their different evolutions of spin-up and spin-down energy levels.