A combinatorial screening method for corrosion research using an ion beam co-sputtering system and a microelectrochemical probe was proposed. Small chips of pure Cr and Mo were placed on a large Fe-11%Cr plate, and those were used as a complex target for co-sputtering. The composition gradients of the sputter-deposited films were found to be controllable by the arrangement and the number of pure Cr and Mo chips. The optimum condition for fabricating Fe-Cr-Mo combinatorial libraries was investigated, and Fe-19%Cr-x%Mo (5<x<48) and Fe-7%Cr-x%Mo (3<x<46) films were prepared. A microelectrochemical technique was applied to measure the corrosion behavior of the restricted small area on the combinatorial libraries. The small diameter of microelectrochemical probes was appropriate for suppressing the measurement error arising from the compositional gradient within an measured area. The influence of Mo content on the polarization behavior of Fe-Cr-Mo alloys in 1 kmol·m−3 H2SO4 and 1 kmol·m−3 NaCl were investigated. The results obtained were similar to those previously reported for bulk Fe-Cr-Ni alloys, which indicated that the combinatorial screening method proposed in this study would be used for high-throughput tests for corrosion research.