Abstract Objective Post-stroke cognitive impairment (PSCI) substantially affects patients’ quality of life. This study explored the therapeutic efficacy of intermittent theta burst stimulation (iTBS) combined with cognitive training for PSCI. Design The experimental group received iTBS and cognitive training, whereas the control group only received cognitive training, both for six weeks. The outcome measures were the Loewenstein Occupational Therapy Cognitive Assessment (LOTCA), Modified Barthel Index (MBI), Transcranial Doppler Ultrasonography (TCD), and Functional Near-infrared Spectroscopy (fNIRS). Results After therapy, between-group comparisons revealed a substantial difference in the LOTCA scores (P = 0.024). Improvements in visuomotor organization and thinking operations were more noticeable in the experimental group than in the other groups (P = 0.017 and P = 0.044, respectively). After treatment, the resistance index of the experimental group differed from that of the control group; channels 29, 37, and 41 were activated(P < 0.05). The active locations were the left dorsolateral prefrontal cortex (DLPFC), prefrontal polar cortex, and left Broca’s region. Conclusion iTBS combined with cognitive training had a superior effect on improving cognitive function and everyday activities compared with cognitive training alone, notably in visuomotor organization and thinking operations. iTBS may enhance cognitive performance by improving network connectivity.