Metal alloys exhibit functionalities unlike those of single metals. Such alloying has drawn considerable research interest, particularly for nanoscale particles (metal clusters/nanoparticles), from the viewpoint of creating new functional nanomaterials. In gas phase cluster research, generated alloy clusters can be spatially separated with atomic precision in vacuum. Thus, the influences of increases or decreases in each element on the overall electronic structure of the cluster can be elucidated. However, to further understand the related mixing and synergistic effects, alloy clusters need to be produced on a large scale and characterized by various techniques. Because alloy clusters protected by thiolate (SR) can be synthesized by chemical methods and are stable in both solution and the solid state, these clusters are ideal study materials to better understand the mixing and synergistic effects. Moreover, the alloy clusters thus created have potential applications as functional materials. Therefore, since 2008, we have been working on establishing a precise synthesis method for SR-protected alloy clusters and elucidating their mixing and synergistic effects. Early research focused on the precise synthesis of alloy clusters wherein some of the Au in the stable SR-protected gold clusters ([Au25(SR)18]- and [Au38(SR)24]0) is replaced by Pd, Ag, or Cu. These studies have shown that Pd, Ag, or Cu substitute at different metal sites. We also have examined the as-synthesized alloy clusters to clarify the effect of substitution by each element on the physical and chemical properties of the clusters. However, in early studies, the number of substitutions could not be controlled with atomic accuracy for [Au25- xM x(SR)18]- (M = Ag or Cu). Then, in following research, methods have been established to obtain alloy clusters with control over the composition. We have succeeded in developing a method for controlling the number of Ag substitutions with atomic precision and thereby elucidating the effect of Ag substitution on the electronic structure of clusters with atomic precision. Concurrently, we also studied alloy clusters containing multiple heteroelements with different preferential substitution sites. These results revealed that the effects of substitution of each element can be superimposed on the cluster by combining multiple elemental substitutions at different sites. In addition, we successfully developed methods to synthesize alloy clusters with heterometal core. These findings are expected to lead to clear design guidelines for developing new functional nanomaterials.