The ternary FePtSn alloy nanoparticles (NPs) were synthesized via a simple programmed microfluidic process, showing a great electrochemical performance in methanol oxidation reaction (MOR). The synthesis process exhibited convenient and spatial-temporal kinetics control of the NPs formation for a narrow size distribution, ultra-small (~2nm) and good dispersion features. The morphology, crystal structure and composition of FePtSn NPs were characterized by transmission electron microscopy (TEM), energy-dispersive X-ray spectroscopy (EDS), powder X-ray diffraction (XRD). FePtSn/C nanocatalyst ink could be further prepared by mixing the as-synthesized or annealed FePtSn NPs with carbon black powder and nafion. Their electrocatalytic performances were tested by the electrochemical work station. By contrast, the annealing treatment made more active sites exposed and facilitated the catalytic performance of FePtSn/C NPs. The electrochemical active surface areas (ECSAs, 42.8m2/g), catalytic activity (If: 588.1 mA/mg-Pt) and electrochemical durability of FePtSn/C nanocatalysts after annealing were greatly improved, comparing with as-synthesized samples and commercial Pt/C nanocatalysts for MOR. In addition, the onset potential of annealed FePtSn/C nanocatalysts was improved, much better than the commercial Pt/C nanocatalysts.