Combination therapy with motor imagery (MI)-based brain-computer interface (BCI) and repetitive transcranial magnetic stimulation (rTMS) is a promising therapy for poststroke neurorehabilitation. However, with patients' individual differences, the clinical effects vary greatly. This study aims to explore the hypothesis that stroke patients show individualized cortical response to rTMS treatments, which determine the effectiveness of rTMS-induced MI decoding enhancement. We applied four kinds of rTMS treatments respectively to four groups of subacute stroke patients, twenty-six patients in total, and observed their EEG dynamics, MI decoding performance, and Fugl-Meyer assessment changes following 2-week neuromodulation. Four treatments consisted of ipsilesional 10 Hz rTMS, contralesional 1 Hz rTMS, ipsilesional 1 Hz rTMS, and sham stimulation. Results showed stroke patients with different neural reorganization patterns responded individually to rTMS therapy. Patients with cortical lesions mostly showed contralesional recruitment and patients without cortical lesions mostly presented ipsilesional focusing. Significant activation increases in the ipsilesional hemisphere (pre: -15.7% ∓ 8.2%, post: -17.3% ∓ 8.1%, p = 0.037) and MI decoding accuracy enhancement (pre: 76.3 ± 13.8%, post: 86.6 ± 8.2%, p = 0.037) were concurrently found in no-cortical-lesion patients with ipsilesional activation treatment. In the group of patients without cortical lesions, recovery rate in those receiving ipsilesional activation therapy (23.5 ± 10.4%) was higher than those receiving ipsilesional suppression therapy (9.9 ± 9.3%) (p = 0.041). This study reveals that tailoring neuromodulation therapy by recognizing cortical activation patterns is promising for improving effectiveness of the combination therapy with BCI and rTMS.