Survivors of stroke often have varying degrees of upper limb motor dysfunction, which limits their independence in daily life. Restoring upper limb motor function is crucial for regaining the ability to perform activities of daily living. Transcranial magnetic stimulation (TMS) is a non-invasive neuromodulation technique that has become an important tool in stroke rehabilitation in recent years. This article reviews the progress in the application of different modes of TMS in the treatment of upper limb motor dysfunction after stroke, including the mechanism of action and therapeutic effects. There is substantial evidence supporting the efficacy of repetitive TMS (rTMS) in improving upper limb motor function, while there is limited research on theta burst stimulation (TBS) and paired associative stimulation (PAS), and their mechanisms are still unclear with controversies regarding their effectiveness. Future research should focus on exploring new targets and optimal treatment parameters for TMS in treating upper limb motor dysfunction after stroke, in order to develop personalized TMS treatment plans for stroke patients.