Noble metal nanocrystals have been extensively utilized as promising catalysts for chemical transformations and energy conversion. One of their significant applications lies in electrode materials in fuel cells (FCs) due to their superior electrocatalytic performance towards the reactions both on anode and cathode. Nowadays, tremendous efforts have been devoted to improve the catalytic performance and minimize the usage of precious metals. Constructing multicomponent noble metal nanocrystals with complex structures provides the opportunity to reach this goal due to their highly tunable compositions and morphologies, leading to the modification of the related electrochemical properties. In this review, we first highlight the recent advances in the controllable synthesis of noble metal alloy complex nanostructures including nanoframes/nanocages, branched structures, concave/convex structures, core-shell structures and ultrathin structures. Then the effects of the well-defined nanocrystals on the modified and improved electrochemical properties are outlined. Finally, we make a conclusion with the points on the challenges and perspectives of the controllable synthesis of noble metal alloy complex nanostructures and their electrocatalytic performance.