This investigation demonstrates the magnetic properties and nanostructures of CoPt3 wire arrays that were fabricated by electrodeposition using a porous alumina template. The X-ray absorption analysis clearly verified the occurrence of a phase transition in CoPt3 nanowires. This phase transition significantly influences the magnetic properties and enhances coercivity and squareness. The phase transition of CoPt3 nanowires was from a random alloy distribution to anisotropically ordered CoPt3 (L1(2)). The thermally induced phase transition of CoPt3 nanowires to ordered L1(2) CoPt3 through a "cluster-in-cluster' intermediate state via interdiffusion processes is revealed. The mechanism exhibited by these CoPt3 nanowires is proposed to explain the strong correlation between their magnetic character and their atomic distribution.