Controlling the spin of metal atoms embedded in molecular systems is a key step toward the realization of molecular electronics and spintronics. Many efforts have been devoted to explore the influencing factors dictating the survival or quenching of a magnetic moment in a metal–organic molecule, and among others, the spin control by axial ligand attachments is the most promising. Herein, from the interplay of high-resolution scanning tunneling microscopy imaging/manipulation and scanning tunneling spectroscopy measurements together with density functional theory calculations, we successfully demonstrate that a Ni trimer within a metal–organic motif acquires a net spin promoted by the adsorption of an on-top Br atom. The spin localization in the trimetal centers bonded to Br was monitored via the Kondo effect. The removal of the Br ligand resulted in the switch from a Kondo ON to a Kondo OFF state. The magnetic state induced by the Br ligand is theoretically attributed to the enhanced Br 4pz and Ni 3dz2 states due to the charge redistribution. The manipulation strategy reported here provides the possibility to explore potential applications of spin-tunable structures in spintronic devices.