Periodic alloyed (Au-Ag, Au-Cu, Au-Ag-Cu) nanoparticle (NP) arrays with uniform size, controllable composition and center-to-center spacing were fabricated by a novel and facile strategy based on physical vapor deposition on a monolayer colloidal crystal template and further heat treatment. The composition and center-to-center spacing were manipulated by adjusting the sputtering target in the deposition process and the size of colloidal spheres of the template, respectively. The shadow effect and a dewetting model were employed to analyze the whole process of evolution from a metallic thin film to spherical nanoparticles with uniform size. The localized surface plasmon resonance (LSPR) and diffraction peaks of these alloyed arrays were systematically measured. The dielectric constant has an important influence on LSPR peaks and diffraction peaks. Both the LSPR and diffraction peaks of Au-Ag alloyed NPs arrays exhibit a blue shift due to their lower dielectric constant than that of pure Au NPs. However, compared with Au, Cu possesses a higher dielectric constant, leading to a red shift of the LSPR and diffraction peaks of Au-Cu alloyed NPs arrays. With the increase of NP size, the diffraction peaks of both binary alloyed NPs exhibit a slight red shift. Moreover, the LSPR absorption peaks were more sensitive to the composition of the NPs than the diffraction peaks. This work would open up a novel strategy in the production of alloyed NP arrays with tunable LSPR peaks and diffraction peaks, which would be very helpful to improve their practical applications in various fields.