Low-noble metal electrocatalysts are attracting massive attention for anode and cathode reactions in fuel cells. Pt transition metal alloy nanostructures have demonstrated their advantages in high performance low-noble metal electrocatalysts due to synergy effects. The basic of designing this type of catalysts lies in understanding structure-performance correlation at the atom and electron level. Herein, design threads of highly active and durable Pt transition metal alloy nanocatalysts are summarized, with highlighting their synthetic realization. Microscopic and electron structure characterization methods and their prospects will be introduced. Recent progress will be discussed in high active and durable Pt transition metal alloy nanocatalysts towards oxygen reduction and methanol oxidation, with their structure-performance correlations illustrated. Lastly, an outlook will be given on promises and challenges in future developing of Pt transition metal alloy nanostructures towards fuel cells catalysis uses.