Halogens have widely served as handles for regulating the growth of nanoparticles and the control of their physicochemical properties. However, their regulatory mechanism is poorly understood. Nanoclusters are the early morphology of nanoparticles and play an important role in revealing the formation and growth of nanoparticles due to their precise structures. Here, we report that halogens induce the anisotropic growth of Ag40(C6H5COO)13(SR)19(CH3CN) (Ag40-II, where SR = 4-tert-butylbenzylmercaptan) into Ag45(C6H5COO)13(SR)22Cl2 (Ag45), where Ag40-II is converted from Ag40(CH3COO)10(SR)22 (Ag40-I). Experiments and theoretical simulations showed that halogen ions adsorb at both ends of the cluster, forming defect sites. The -SR-Ag- complexes fill the defects and complete the anisotropic transition from Ag40-II to Ag45. Circular dichroism spectra show that the chirality of Ag45 decreases 15-fold compared with that of Ag40-II. This work provides important insights into the effects of halogens on the growth mechanism and property regulation for nanomaterials at the atomic level and the benefits of further applications of halogen-induced nanomaterials.