The use of ligand-protected gold clusters for catalysis has been extensively researched in catalysis due to their excellent properties, stability, and ability to maintain a precise atomic number. However, the role of ligand effects in the catalytic process remains unclear. Therefore, there is a need to understand how ligands modulate the electronic structure and catalytic properties of gold clusters. In this study, we selected four experimentally produced phosphorus ligand-protected gold clusters ([Au9(PPh3)8]3+, [Au10(PPhCy2)6Cl3]+, [Au11(PPh3)8Cl2]+, and [Au13(PMe2Ph)10Cl2]3+). We performed first-principles calculations to investigate the changes in the geometry and electronic structure of these clusters during the shedding of ligands. In addition, we characterized their catalytic properties using CO oxidation reactions. Our results show that the small-sized ligand-protected gold clusters exhibit an evolutionary trend towards a planar structure with the shedding of ligands. The d orbital centers and O2 adsorption of these clusters also exhibit a unique linear relationship. Furthermore, these ligand clusters exhibit excellent CO oxidation activity through both L-H and E-R mechanisms, with several representative catalytic reactions having reaction barriers ranging from 0.38 eV to 0.78 eV. The catalytic activity demonstrates a distinct relationship with the adsorption energy and d orbital centers. Importantly, our findings suggest that it is possible to regulate the geometry, electronic structure, and catalytic activity of ligand-protected gold clusters.