Colloidal bimetallic nanoclusters of $\mathrm{Au}-\mathrm{Pd}$ were synthesized by simultaneous reduction of the metal ions from their corresponding chloride salts with polymer (PVP) stabilizer. Structural characterization of the samples with different $\mathrm{Au}∕\mathrm{Pd}$ ratios was made using high-resolution electron microscopy. Classical molecular dynamics simulation is used for structural thermodynamics and dynamic analysis of the bimetallic clusters. Structural incoherency and structure reversal mechanism in such bimetallic clusters were studied systematically for different atomic configurations, which explain the anomalies on the reported experimental results on such nanoclusters mainly by electron microscopy. Our simulation and experimental results revealed that stable ordered structures of the bimetallic cluster are Pd core/Au shell, random solid solutions and eutecticlike configurations. Though the Au-core/Pd-shell structure is stable at low temperature, the structure changes to Pd core/Au shell on heating at about $500\mathrm{K}$.