The ligand exchange-induced size/structural transformation (LEIST) reaction of metal nanoclusters gives researchers an effective way to understand the structural transition, broaden the methods of synthesis, and enhance the relevant performance of metal nanoclusters. Herein, the structural features and unique bonding modes of phosphine ligands are investigated to explore the phosphine-LEIST reaction, which shows an advantage in metal nanocluster’ structural modification and property modulation. This review focuses on the phosphine LEIST and the corresponding catalytic and optical performance regulation of metal nanoclusters. An introspective outlook is also presented concerning the design and synthesis of functional phosphine ligands for the further evolution in modulates and performance of atomically precise metal nanoclusters.