The effect of trace Cu element additions on the properties of Pd-based amorphous alloys was investigated by a combination of experimental and molecular dynamics (MD) simulations. Thin ribbons of Pd40Ni40P20 and containing different proportions of Cu (1 %, 3 %, and 5 %) were prepared, analyzed by X-ray diffraction (XRD) to determine the phase structure, tested for their thermal properties by differential scanning calorimetry (DSC), and nanoindentation to test their mechanical properties. Meanwhile, the amorphization process and compression behavior of these alloys were simulated by MD simulation, and the microstructures of the alloys were resolved by using the radial distribution function (RDF) and the coordination number distribution function (PDF), and the glass transition temperatures (Tg) were deduced from the energy variations. The Voronoi polyhedral analyses showed that the addition of trace amounts of Cu altered the content of the specific clusters, which affected the macroscopic mechanical properties. Both nanoindentation experimental and simulation results confirmed that the addition of trace Cu reduces the Tg and improved the mechanical properties of the Pd40Ni40P20 alloy while maintaining the amorphous structure.