Objective To explore the efficacy of multi-target sequential repetitive transcranial magnetic stimulation (rTMS) combined with task-oriented training (TOT) on upper limb dysfunction after stroke. Methods The clinical data of 85 patients with upper limb dysfunction after stroke who received treatment in the rehabilitation department of our hospital from August 2023 to August 2025 were retrospectively collected. According to the different intervention schemes, the patients were divided into the control group (receiving conventional rTMS combined with TOT, n = 45) and the observation group (adopting multi-target sequential rTMS combined with TOT, n = 40). The upper limb motor function [Fugl-Meyer upper limb motor function assessment scale (FMA-UE), Action Research Arm Test (ARAT)], upper limb motor ability [Wolf motor function test (WMFT)], daily living activity ability [modified Barthel index (MBI)], and adverse reactions were analyzed and compared between the two groups before treatment, at the end of 4 weeks of treatment, and 3 months after treatment. Results At the end of 4 weeks of treatment and 3 months after treatment, the FMA-UE and ARAT scores of both groups were significantly higher than those before treatment, and the WMFT of the observation group was obvious lower than control group at all time points (P < 0.05). At the end of 4 weeks of treatment and 3 months after treatment, the MBI scores of both groups were obvious higher than before treatment (P < 0.05), and the MBI scores of the observation group were obvious higher than control group at all time points (P < 0.05). There was no obvious difference in the incidence of adverse reactions between the two groups (P > 0.05). Conclusion The multi-target sequential rTMS combined with task-oriented training scheme can improve the upper limb motor function and daily living activity ability of stroke patients, and has a high safety profile.