While Transcranial Magnetic Stimulation (TMS) shows therapeutic potential for Alzheimer’s Disease (AD), its mechanisms of action remain unclear. This study investigated TMS-induced brain network restructuring in 17 AD patients by analyzing resting-state fMRI before and after 20 Hz treatment, identifying regions of interest (ROIs) based on ALFF and fALFF changes. Subsequently, functional connectivity (FC) analyses were conducted based on these ROIs. At a global level, topological properties and FC between sub-networks were also analyzed. Our findings revealed increased ALFF and fALFF in the right dorsolateral prefrontal gyrus and the left anterior cingulate gyrus. Using the right dorsolateral prefrontal gyrus as a seed, we observed enhanced FC with the right middle temporal gyrus, which was related to improved cognitive performance. Similarly, using the left anterior cingulate gyrus as a seed, we found decreased FC with the left inferior temporal gyrus, correlating with improvements in semantic understanding. From a global perspective, AD patients exhibited a significant increase in clustering coefficient and strengthened FC between the dorsal and ventral attention networks (DAN/VAN). These results suggest that TMS may regulate cross-regional functional collaboration, enhance the integration of key subnetworks, and promote comprehensive improvement in patients’ cognitive abilities.