The precise manipulation of nanocluster structures remains highly desirable for disclosing the structure-property correlations at the atomic level. However, the control over a nanocluster (metal kernel + surface ligand) with a maintained template has long been a challenging pursuit, and little has been achieved for manipulation at the atomic level. Here, on the basis of the M29(SR)18(PR'3)4 cluster system, the control over the vertex phosphine ligands is accomplished. Therefore, a combination of the manipulation of vertex phosphines in this work and of internal metals and surface thiols reported previously realizes control over the M29(SR)18(PR'3)4 cluster template. The principles for regulating the photoluminescence (PL) of M29 clusters via dictation of their metal compositions, surface thiols, and vertex phosphines are exploited to rationally design the most emissive nanocluster among the M29 cluster family. Overall, this work fills the missing part necessary for the manipulation of M29(SR)18(PR'3)4 nanoclusters, providing an ideal nanomodel that enables us to grasp the structure-property correlations at the atomic level.