Au–Pd–Zr ternary alloy phase diagram at 25 °C was calculated by Panda phase calculation software, and the thermodynamic data were based on three binary alloy phase diagrams: Pd–Au, Au–Zr, and Pd–Zr. Five composition points in the ternary phase diagram were selected to predict the precipitation order. One (32Au–32Pd–36Zr) of the five composition points in ternary phase diagram was chosen to verify the correctness of the phase diagram calculation and the precipitation order by scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), and X-ray diffraction (XRD). The unknown phase in XRD patterns was predicated by EDS and materials studio (MS) software. The experimental results show that there are seven key ternary reactions points and 17 phase regions in all isothermal sections at 25 °C. The thermodynamic process and microstructure for the alloy phase can be described in order according to the vertical section in phase diagram. The phase compositions of the chosen one point are consistent with calculation prediction. The unknown phase in XRD patterns should be Zr2AuPd by the first principle X-ray simulation.