With considerable attention focusing on metal nanoclusters, to explore the relationship of structures and their properties is of prime importance for designing novel functional nanoclusters and promoting their applications. Here we reported two novel alloy nanoclusters, [Pt₁Ag₂₄(SR)₂₀]⁴– and Pt₁Ag₁₄(SR)₆(PPh₃)₈ (H-SR: 2-chloro-4-fluorobenzenethiol), determined by X-ray crystallography. Interestingly, the two alloy nanoclusters have the same centered icosahedral Pt₁Ag₁₂ kernel, but shell structures are totally different due to the addition of PPh₃ in the synthesis. Upon removal of the kernel, the shell of the Pt₁Ag₂₄ nanocluster is composed of two unique trefoil-like Ag₆(SR)₁₀ motifs, while the Pt₁Ag₁₄ nanocluster has six PPh₃ and two Ag(SR)₃(PPh₃) motifs. Furthermore, fluorescence spectroscopy and ultraviolet–visible absorption spectroscopy (UV–vis) were carried out to investigate the optical properties. The Pt₁Ag₂₄ nanocluster has near-infrared photoluminescence at 738 nm, whereas the emission of the Pt₁Ag₁₄ nanocluster is at 639 nm, demonstrating a blue shift of 99 nm. The two nanoclusters exhibit distinct optical fingerprints. Furthermore, the predicted partial density of states and UV–vis spectra assignments reveal the relationship of the crystal structures, electronic structures, and optical properties. These findings not only provide a feasible strategy to synthesize functional metal nanoclusters with distinctive structures but also give direct insight into understanding the structure–property correlations at the atomic level.