Platinum-based alloy nanocatalysts are highly attractive for both heterogeneous catalysis and electrocatalysis. However, their stability remains a major concern for their application under realistic operating conditions. We herein report a microwave-assisted synthesis of atomically ordered Ru-core Pt-shell (Ru@Pt) nanoparticles that show superior catalytic properties for methanol electrooxidation. The Ru@Pt catalysts are found to display higher methanol oxidation activity and CO-deactivation resistance than the commercial Pt–Ru catalysts. Shell-thickness variation induced properties is of great importance for core–shell catalysis. Above all, well-ordered Ru@Pt with sub-nm Pt shell exhibit superior durability in long-term and extreme operation condition in direct methanol fuel cell (DMFC). This type of core–shell catalysts thus hold great potential to be applied as high performance anode catalysts in DMFCs.