The detailed elucidation of structure–property relationships at the molecular level in metal nanoclusters is highly valuable for advancing structure design and optimizing performance. However, effectively manipulating metal nanoclusters’ physical and chemical properties at the single-molecule level remains a significant challenge. Here, we demonstrate that single-molecule chemistry can effectively control the third-order nonlinear optical (NLO) performance of structurally precise copper nanoclusters. We present two analogous clusters, [Cu₂₅(RS)₁₈H₁₀]³⁻ (Cu₂₅) and [Cu₂₆(RS)₁₈H₁₀(PPh₃)]²⁻ (Cu₂₆, where RSH is 2-fluorobenzenethiol), whose structures were determined in this study. Both clusters feature a Cu₁₃ core in a centered cuboctahedron configuration with similar shell structures. However, Cu₂₆ includes an additional PPh₃Cu⁺ unit. This single structural difference significantly changes their properties, including optical characteristics and stability. Compared to Cu₂₅, Cu₂₆ exhibits enhanced optical limiting (OL) activity. Theoretical calculations indicate that the substantial electron transfer from the PPh₃ ligand to the metal core enhances the NLO performance of Cu₂₆. This study highlights the potential of structurally precise copper nanoclusters as OL materials and advances the understanding of nanoparticulate material fabrication using a single-molecule strategy.